Taken by Storm
by flyboyfan23
Summary: Sheppard has been missing for nearly a week,held prisoner in a remote jungle. It comes to everyone's surprise when he comes stumbling through the stargate with a companion in tow, a very furry companion. shep whump AU in some ways,but the basicsarethesame
1. Chapter 1

**I'm back! Sorry to everyone that was following my other story "The Other Side". I won't be returning to it for a while at least, too much came up and I have lost any inspiration I did have with it. Maybe someday I'll continue. **

**But, anyways this is my new one and I hope you all will like it. I'm hoping to update every other day or so, but don't hold me to it, and I'm hoping the chapters will be of decent size. Well, hope you enjoy it. Not much whump in this chapter but we'll get there. **

** Taken by Storm**

Sheppard groaned as he rolled over in his bed, the blanket bunched up to reveal his bare feet which , as usual, were dangling off the end of the mattress. Both Ronon and he had decided the Ancients had been a short race because all the beds were a good four inches shorter than standard on Earth. The Dedalus was now making regular runs in between the two galaxies and John's first request was for new bed frames and mattresses to fit. His second simply another case of popcorn since Teyla had eaten his last bag. He regretted ever inducing that woman to the salty snack, as she all but inhaled each kernel.

Slowly, an arm emerged from the blankets to fumble along the bedside table in search of the alarm clock which was emitting the highly offensive noise that had roused him. Normally the Colonel was an early riser, getting a few miles in before breakfast but today was the day his reports were due. Reports which were stacked in a rather large pile, untouched on his desk. Though many would call him crazy, the thought of the hours of paperwork sitting there, waiting for him, was more intimidating than facing down an army of wraith. Paper cuts were painful after all.

Groaning, Sheppard pulled the covers off his body before shuffling over to his bathroom, thinking it best to get the torture done as soon as possible, but that was only if he could get Elizabeth to let it slid for a couple more days.

"No, John." Weir's voice was unwavering as Sheppard entered her office, a familiar lazy grin on his lips.

"Why do you think I was gonna ask you something?" He replied, sitting in the chair in front of her desk. "Can't a guy just say good morning?"

"Not when the monthly reports are due tomorrow. So, no. I need those reports today." Elizabeth replied, sitting back in her seat and crossing her arms.

"Come on, Elizabeth. I just need two more days. That's all." He attempted to give her his best kicked puppy impression.

"No, Colonel, I need those reports by midnight tonight. That gives you the entire day." Elizabeth held up a hand, stopping John as he opened his mouth to speak. "And there will be no missions until those reports are in my inbox, completed and filed correctly."

John sighed, realizing there was no way out of this. Weir could not help but smirk as he rose and slowly walked out of the office, mumbling under his breath about the Geneva convention as well as cruel and unusual punishment.

He had only made it a few steps from the door when the 'gate erupted into activity and the alarm sounded.

Weir sighed as she pushed herself out of her chair, following John to the control room. "What do we have, Chuck?"

"It's Lorne's team, ma'am. They're sending us a transmission." The technician stated, fingers flying over the console.

"Bring it up." Elizabeth said, even as the screen in front of her sprung to life, showing a very grim Major Lorne.

"Dr. Weir, I'm afraid we have a bit of a situation here" His voice echoed slightly over the speakers.

"What kind of situation, Major?" Sheppard cut in instantly, unable to disguise the concern for him men in his voice. He took his position seriously and while most commanding officers were only concerned about climbing the ladder, John did and always would put his men first.

"Guerilla warfare, sir." Lorne answered. "Seems some of the locals don't appreciate outside help. They're afraid it will attract the attentions of the wraith."

"I don't think I like where this is going.." Sheppard mumbled.

"No, sir. You won't." Evan answered. "They attacked us, grabbed Clarke and disappeared into the jungle."

"Did you try and track them?" John asked, shifting from back and forth on the balls of his feet, anxious to get to the planet and find the lost lieutenant.

"Simmons and Lawson are on it now, sir."

Elizabeth's frown deepened when she heard this. "You sent them in without backup?"

Lorne quickly shook his head, not ever wanting to be on Weir's bad side. Everyone had seen and felt the effects when one of the marines decided to bring a potentially dangerous marsupial to Atlantis, claiming it had climbed into his backpack unbeknown to him. The man still back away slightly whenever in the same room with her. "No, ma'am. They are just scanning the perimeter until told otherwise."

"I'll be there with a team by 0900, Major." Sheppard answered before signaling for Chuck to cut the transmission.

"Take Garrett's team, Colonel. Lt. Peters was just released to active duty."

Sheppard nodded, quickly turning on his heels before spinning back around when she called him.

"And Colonel, looks like you got out of that paperwork, but I expect it the instant you're back." She said, crossing her arms in front of her, a small smile tugging at the corner of her mouth.

Sheppard's own sideways grin broke through his lips as he realized the unexpected escape that had been thrown in his face.

"I'll give you a call when we get him." He told her before running down the stairs. She was about to stop him, reminding John that she needed a few more check-ins than that, but he had already disappeared.

"Alright guys, stay sharp." The Colonel ordered his men as they carefully trekked through the jungle, each man looking for any sign of their missing companion. The rather large group slowly picked their way through the dense vegetation, making as little noise as possible so as not to attract unwanted attention. Ronon was only a few yards away from Sheppard, attempting to glean any clues from a jungle that seems insistent to keep her secrets to herself.

"This would be easier if it hadn't rained." The Satedan grumbled and he lifted the leaves of a fern-like plant to peer at the mud slicked ground.

"Wouldn't the mud make it easier, you know, tracks and all?" McKay snapped sarcastically.

Ronon straightened and turned towards him with a glare, before growling. "When it's a typical rain, yes, but not with a torrential down pour. Washes away all the tracks."

"Remind me again why we can not just track Clarke by the sub-q transmitter?" Teyla asked, delicately stepping over a very unpleasant pile of rotting leaves and mud.

Rodney gave a very exaggerated sigh as though he had explained this many times before. Which he had, to Sheppard many times. In truth, John just knew how to irritate the snot out of the scientist and really tried his best as a simple hobby.

"Because..." McKay answered, drawing a few more syllables from the single word with annoyance. "The atmosphere in the forest is charged with enough electricity, generated by the ever present storms clouds is enough to scramble any frequencies. Stupid that the so-called all-knowing ancients couldn't even figure how to work around that in their ships." The Canadian finished grumbling.

"It's not like you could do it either." Sheppard mumbled, without looking up, instead watching the littered terrain for clues.

Rodney stopped suddenly in his tracts and point a finger at the Colonel. "That's not my point!" He snapped, his pride wounded. He would have continued if not for Teyla setting her hand gently on his shoulder.

"We know what you mean, Rodney." She said while sending a warning glare towards Sheppard, who quickly tried to hide his smirk.

The teams searched in silence for near two more hours, finding their way deeper into the dense jungle. Though they had began as soon as possible, which had still been fairly early in the afternoon, they now found themselves in the high heat of the day. The air hung thickly around them, a person's lungs protesting even the shallowest of breaths.

"Maybe it's time to head back" John mumbled, discouraged at the lack of progress. "We'll try the other area around the 'gate to the north." Like most planets in the Pegasus galaxy, local villages would set up far from the stargate, hoping to escape a wraith culling.

Slowly the group turned back to the path they had been following, their guard down, seeing as they had already scanned this area.

"Stupid electric storms and their stupid rain." Rodney mumbled as the clouds suddenly burst open and a mild shower began to fall around them.

"Stop your grumbling McK-" Sheppard was cut off by Ronon, who raised a hand staring into the underbrush in front of them.

"Someone's out there." The Satedan managed to hiss under his breath seconds before the air broke out with the clatter of gun fire. The team scattered, diving for cover while simultaneously raising their weapons.

"Where are they?" Rodney's voice was strained to be heard over the weapon discharge.

Ronon grunted, aiming into the trees in front of them then shot. The red flare did not miss it's target and a well camouflaged man fell from the underbrush. "Our 12 is clear." He growled.

"Alright, go!" Sheppard ordered, waiting as Ronon, McKay, and Teyla scrambled through the trees, crouched so as not to be hit.

"Sheppard to all teams, fall back. Under enemy fire, repeat. We are under enemy fire-" John shouted into the radio, hoping his message would break through the highly charged atmosphere. He was close behind his team when a stunner caught his leg, causing him to fall face first into the leaf strewn ground.

"SHEPPARD!" Ronon's gruff voice seemed to echo through the forest over the weapon's clatter.

"GO!" John shouted, waving a hand to motion them forward, before another blast hit his shoulder, effectively immobilizing him.

"Ronon! We must go." Teyla insisted, pulling the large man by the arm.

"No, we need to get Sheppard!"

Teyla tugged harder, her nails digging into his flesh. "We do not know how many there are. We will come back!"

Laying there, his face in the mud, he could only listen and hope his team escaped safely as their voices faded. Large, mud-covered boots were the last thing the Colonel saw, before darkness overtook him.

**Well, there you have it: the set up. Now review so I know people are listening!**


	2. Chapter 2

**Thanks to everyone who reviewed! Hope you all like this chapter, not much Sheppard but he'll be coming so don't worry!**

Major Lorne stifled a yawn as he exited the small hut he and the rest of the Atlantis resistance had taken shelter in for the night. The morning sun warmed his skin and he took a deep breath of the fresh air that held that crisp taste that only came after a rainstorm. He could hear his team rummaging back inside, strapping on gear and preparing to further the search for the Colonel and Clarke. Days had passed since Sheppard's kidnapping and there still was no sign of either man. Rodney had returned to Atlantis in order to work on a solution around the electrical storms, but to no avail as of yet.

Noticing a dark figure silhouetted against the first rays of the sunrise, he raised a hand to blocked the blinding light, expecting to find Ronon a few meters in front of him. The Satedan had risen before sunrise each day along with Teyla, in hopes of catching a glimpse of a camp fire in the thick trees but that too had proven useless. It was obvious that the captors were deep into the heart of the jungle, far from the usual trails made by the villagers.

Lorne took a step closer to the silhouette, quickly realizing that this was not Ronon but Clarke who was strung with his hands above his head to the single village well.

"LAWSON!" Evan bellowed for his team's medic, his weapons immediately raised as he scanned the villager perimeter. Nothing odd stood out to the Major, no obvious dangers at the moment, so he allowed himself to examine his comrade. His arms were stretched far above his head, his right elbow bending at a very awkward position. Blood matted his hair as well as the left side of his face and Evan could not find a single section of unbruised flesh. His shirt was missing, revealing a series of deep incisions, disturbingly neat and straight, were scored along his chest. A large gash was also missing from his side, a thick line of dried blood leading down to the hem of his pants. Lorne hesitantly reached two fingers out to feel below the man's jaw, his hand shaking slightly from the shock. It wasn't that he expected to find a pulse, the damage was far to extensive, but the movement came out of instinct.

"Major, is that?" Evan barely heard Lawson's quiet question as his team including Ronon and Teyla walked up behind him. The medic slowly stepped up to Clarke's body.

"He's dead." Lawson mumbled, again stating what just needed to be said.

Ronon growled under his breath as Lorne and Lawson untied their man before laying him, gently, on the ground.

"How did this happen?" Lorne's whisper was delivered in a very harsh manner, demanding to know how the very beings they were tracking, with all the resources of Atlantis, could simply waltz into the village square without them noticing. "Nobody noticed anything last night? Absolutely nothing?"

"No sir." Simmons replied.

"I did not notice a thing during my shift." Teyla repeated, a slight tremor of fear in her voice. The fact that not only had the guerilla warriors been in the camp, but after seeing the state Lt. Clarke had returned in, she could not help but picture John lying at feet instead.

"We have to find him." Ronon stated in his low voice.

"They found Clarke." Elizabeth said softly as she walked into the lab, where Rodney was busily typing away at his computer. The scientist's neck nearly snapped as he looked up at her words.

"How is he? What happened?" Rodney began his questions immediately. "Does he know where Sheppard is? How did he get away?"

"Rodney, he's dead."

"Oh," McKay's rambling stopped instantly as he realized the implications of her sentence. Though he would never admit it, fear had his gut in it's cold grasp. Clarke has only been gone for a few days yet he was already dead. They didn't have much time before Sheppard's time would run out.

Rodney once again snapped to his desktop, his fingers flying over the keyboard at a furious pace.

"Teyla will be returning to care for Torren, but I am sure she would deeply appreciate anything she can do to help you out." Weir mentioned before leaving, both of them knowing that the Athosian would be 'slightly' anxious to help in any way she could, even though she could not be in the field at the moment.

Teyla could not help but sigh as she looked down at the jungle lay out in her hands. Miles of thick vegetation only rarely broken by rocky outcroppings. There were plenty of places to hide even a large camp.

She looked down at the small sleeping child in the makeshift cradle near her feet. A small blanket was wrapped tightly in his fists, the fabric, being the same shade blue as a clear Atlantis sky at high noon, was covering half his face. It had been a gift from John. He had seen one of the nurses knitting during her night shift while suffering through one of his extended stays in the Infirmary and after much convincing, she had taught him how to knit. An odd hobby for an Air Force Colonel to take up for sure, and he had not been very good at it, always dropping stitches with his too large of hands, but he had finished this one blanket while distracting himself from the daunting accomplishment of healing. Torren had latched onto the blanket instantly, never allowing it from his sight.

A frustrated growl echoed lowly through the conference room. The Athosian's lips cracked in a half-hearted smile as the man responsible for the groan, furiously typing away on the keyboard in front of him. It was an action she saw of him everyday. The computer was simply a further extension of the scientist. It was Rodney's expression that kept Teyla's smirk from turning into a true smile.

McKay's lips were pressed firmly together, forming thin lines. His forehead was furrowed. While the scientist was not known for his happy go-lucky attitude, his face was unusually haunted with guilt and worry.

"Should have figured it out..needed to figure it out.." Teyla's sharp ears picked up his muttering.

She would have disagreed with him, told him it was not his fault but it would do no good. The man was not going to listen to her, the only thing on his mind was to find his missing C.O.

"Unscheduled off-world activation." Echoed through the room but even that could not draw him from his work. He had holed himself up in the conference room claiming his lab to be too noisy and his staff far too ignorant.

Teyla was beginning to believe that nothing would pull Rodney from his work until...

**Sorry for the short chapter! They'll get longer, I promise. Just let me know if there are any missing words and I'll correct them :) Please review! It makes the chapters come quicker!**


	3. Chapter 3

**Next chapter! You get a bit more Shep in here, so have fun.**

**Thanks to everyone for all the reviews, you're all great! And thanks a ton to Joanie x Jony for the original plot idea. Hope you like where I'm taking it. **

Elizabeth yawned, running a hand through her hair. Guilt had it's ice cold fingers wrapped around her intestines. She had been forced to pull her people off the planet, even taking half the villagers in, in order to seek refuge from a huge tropical storm that had hit without warning. The torrential downpour was only half the problem because the electrically charged atmosphere had grown unstable, proving to dangerous for the team to remain on planet. She had pulled everyone out, everyone except John.

The Colonel was still missing, even after days of searching with all the resources at their disposal. She was losing options quickly. They wouldn't give up their search but the jungle was getting denser with each step and the deeper they explored the chances of someone else disappearing increased greatly. She wasn't sure how much longer she could justify the risk.

Nearly growling in frustration, Weir settled her forehead in the crook of her arm, effectively hiding from the world, if only for a few minutes. Unfortunately her serenity was quickly broken as the alarms sounded in warning of a incoming traveler.

"Unscheduled off world activation!" Chuck voiced stated over the intercom.

"Who is, Chuck?" Elizabeth asked, walking up behind the technician.

Chuck seemed stunned when he received the IDC, simply staring at the screen. "It's..uh, it's Colonel Sheppard, ma'am."

Now it was Elizabeth's turn to looked shocked, not even noticing as Ronon stepped up behind her.

"Should I let him through ma'am?"

"Ugh, yes, yes let him through." Elizabeth answered before leaning forward into the microphone. "I need everyone on high alert." She ordered all the soldiers in the 'gate room even as Ronon drew his own weapon and rushed down the stairs to take cover near the 'gate.

All eyes were trained on the stargate, waiting for someone to arrive. The thought that was clearly on everyone's mind was simple: friend or foe. They couldn't be sure the guerilla rebels did not decide to bring the fight to them or if John had managed to escape by some miracle, but there was always the chance they were sending him back, like they had with Clarke.

Everyone in the room took a sharp intake of breath as Sheppard staggered forward, breaking the event horizon and nearly dropping the average sized dog, who was cradled tightly in his arms. The moment John had crossed the threshold and the cool air of Atlantis hit him, causing him to begin shaking no matter how over-heated his skin was. He quickly took a step back as he noticed a group of people approaching him, unsure if he could trust them. Silence hovered through the 'gate room, broken only by the occasional drip against the floor as it fell from John's rain soaked clothing.

The Colonel's appearance had understandably came as a shock to everyone in the 'gate room, though they had been some-what expected it. As it stood, the on-duty marines were half-heartedly raising their weapons, unsure if they should let their guard down yet, while Elizabeth and Ronon stood a good five feet away, afraid to startle him. Sheppard's gaze seemed to be staring through them, his eyes glazed over.

Weir's eyes scanned the man in front of her, taking in his ragged condition. His pants legs were torn while his shirt was missing and Elizabeth's mind flashed back to Lt. Clarke's body. Mud and grim was clinging to him but she could see deep bruising underneath it all. He was holding his left arm close to his body, managing to support most of the weight of his burden on his right arm, and she could see a disturbing amount of blood at his hairline and covering the right side of his face. While Elizabeth noticed all this, what truly caught her attention were two bloody gashes along each side of his mouth. The only thing she could compare it to were the scars the Joker, Batman's arch nemisis, so proudly sported. They were still seeping rivulets of blood down his chin before soaking in a narrow piece of cloth that hung loosely around his neck.

"John?" Elizabeth's hesitant whisper seemed closer to a yell in the large, quiet room.

The voice, however, seemed to break the man out of his trance and his eyes focused for the first time.

"El'z'b'th?" His reply was mumbled, and barely heard. "Home?"

"Yes John, you're home." She answered him, softly.

A ghost of a smile broke John's cracked lips, even as he fell to the ground, unmoving.

"John!" Weir gasped as he fell, both Ronon and her running forward to the fallen Colonel but were stopped almost instantly by a low growling.

SGASGASGAGSAGSASGASGA

He wasn't sure what exactly was going on but he knew his friend couldn't protect himself and they were surrounded. The canine recognized weapons when he saw them, having been on the receiving end of such things. As it was his back leg was burning, the bullet still lodged within his muscle, but easily pushed the pain aside. He would focus on it when both he and the kind man were safe.

The canine had learned quickly in his life not to trust humans. They had proven time and again that any attention from them meant pain. He had thought that of his friend at first. Watching as he attempted to fight against the members of his own pack, turning on his own kind.

He had stalked them, as they tied the man down, one of their own, and attacked him again and again but he had not felt pity for him, not at first. The canine had only hoped to steal some of the carcass from the human pack once they had killed the man. It was not an honorable hunt but he had to survive.

All that changed, however, when the unfortunate human had stood up for him, helped him escape when the pack had turned own him. So he was not about to abandon his new-found friend to another, possibly more ruthless human pack.

They were the pack now, given an odd one, but a pack all the same.

The four legged companion's sharp eyes quickly noticed the approaching people, the woman was not a concern. He had never known the female of this species to be cruel, but he was wary of the large male next to her. He, with his huge muscles and long hair, reminded the canine greatly of his friend's former captors.

His lips raised into a deep snarl, he was not going to allow his friend to be hurt again. He put everything behind his threat, willing to do whatever it took to keep the man safe.

SGASGASGASGASGASGA

Both Ronon and Elizabeth stumbled to a halt as a filthy black creature jumped in front of the Colonel, lips raised in a very threatening snarl. The Satedan beside her, with the testosterone always burning through his veins, stepped forward once again, baring his own teeth. Weir gave a startled jump as the canine gave a sharp demanding bark.

"Ronon, don't." She said, placing a hand on his bicep.

"Bloody-" Came a thick Scottish brogue from behind her. She hadn't even thought about calling the infirmary, having been to caught up in the moment, but apparently someone had. "Elizabeth, I need to get to him now. His breathing is erratic."

Weir gave a small nod. "Ronon, stun it." She stated. It wasn't often that she gave him those orders but he did not hesitate to follow through. The dog fell into a limp pile, caught off guard as he warily watched the entire room.

"All right," The doctor jumped to work immediately, dashing forward and taking his patients pulse. "Stephanie, get him on oxygen. Kevin, help me get him on the gurney and Sarah, begin prepping surgery just in case." Carson gave only a slight pause at he looked at the canine, who having been protecting John, had fallen close by. "Before that Sarah, set this critter up somewhere, he's gonna be in need of some attention as well I imagine." There was a scramble of activity and in mere seconds the Colonel was whisked away down the corridor, leaving Weir and Ronon staring at the floor which was now smeared with a mixture of mud and blood. They only looked up as McKay and Teyla came running down the stairs, Teyla still cradling Torren.

"Where is he?" McKay demanded, taking in deep breaths as he spoke. "And why didn't you tell us he was here? Chuck had to call us!"

"I'm sure they had good reason, Rodney." Teyla cut in, bouncing her slightly cranky son on her hip. He did not appreciate being woken from his nap, only to run through Atlantis in his mother's arms. "Where is the Colonel now?" She then asked in a much less insisting tone.

**I was going to leave you with a bit more of a cliff hanger but it ended up too short. oh well. let me know how I did!**


	4. Chapter 4

**Alright, I know it's been a while and this is a shorter chapter, but my computer all but exploded so I had to rewrite what I had. I can not talk computer, so hopefully I get it fixed soon and post more often. **

"How is he doing, Carson?" Elizabeth asked as she entered the doctor's office.

Sheppard had made it through surgery without a hitch, a rare event when it came to the Colonel. With a few tears in his liver causing minor internal bleeding as well as an array of severely bruised organs, his kidneys facing the brunt of it.

While it sounded like a lot for one body to take, and for most it was, but compared to all the extensive injuries John had dealt with before, these were minor. It was one of the few times that they did not have the over-shadowing fear of John's death and, truth be told, the doctor was reveling in the feeling.

"The lad came through with flying colors. A wee bit of rest and he'll be a good as gold." Beckett smiled before getting up from his chair and walking from behind the desk. "Now, that doesn't mean he doesn't have a long road ahead him, that arm for one is gonna take awhile."

Elizabeth nodded. "I'll be sure to let his team know. They all are very anxious to see him."

"He'll be asleep for another hour or so, but I'm sure he wouldn't be minding a little company."

"I'm sure I won't have any problem rounding up a few volunteers." Elizabeth smirked as she headed towards the exit, stopping just inside the doorway." And what of our furry friend down in isolation? How is he doing?..It is a he, right?"

"Aye, the poor mutt has been through a nightmare but he should make a full recovery. He was shot in the hind leg which required surgery to remove the bullet as well as amputate his tail. It was badly burned and most of it was necrotic.." Carson was going to continue for what was sure to be a long-winded medical diagnosis but Weir interrupted him.

"And a bath?" She asked, picturing the black, muddy canine still poised protectively over Sheppard's fallen body.

"Of course." Beckett smiled. "You don't think I would let him go through surgery looking the way he did, do ya? You'll never guess what color the lad is."

Elizabeth signaled for him to continue when Beckett's dramatic pause grew too long.

"Well, he is black but he also has large white splotches. He's a ringer for your ever intelligent Border Collie."

"Then he should make you feel right at home." Having grown-up in Scotland, the good doctor had often regaled stories of his boyhood playmate, who also happened to be a frisky collie.

"Aye, but the poor bugger is terrified, won't let anyone near him." The kind hearted doctor's face fell, his fingers playing absentmindedly with the end of a thick bandage over the side of his hand and covering his pinky. The small creature had cowered from him, blackened tail between his legs and a snarl on his lips. One contraindicating the other but working in harmony all the same. Although he attempted to appear threatening, not wanting to look like easy prey, he also did not want to attract any attention.

Carson had approached him slowly, crouching low with his hand extended. Needless to say, he had not yet earned the canine's trust.

"He did that." It was stated as a fact instead of a question, Elizabeth having noticed his injured hand.

Carson nodded, remaining in silence for a few minutes, both contemplating the extent of the abuse each of the patients had gone through. You could tell a great deal about a culture by how they treat animals and children. Needless to say Elizabeth was not impressed with this particular group.

"I'll let the team know that you're allowing visitors. I'm sure you'll be seeing each of them rather quickly." Weir replied.

I'm sure I will." He smiled, before giving her a calculating stare. "And you, I want to get a good night's sleep, and don't try and tell me you're not tired. You have not had a full eight hours since the lad disappeared.

A good night's sleep sounds wonderful." She yawned at the mere thought. "Good night, Carson."

"G'night lass."

SGASGASGASGA

Teyla smiled as she approached Ronon and Rodney, both of their trays piled high with a large assortment of food. Perched on Ronon's knee sat Torren, giggling as the scientist across the table shoveled more food into his mouth.

Th scene was not terribly unusual, the team often ate meals together, but the table had been quiet for the past week. Even Torren had barely smirked, picking up on the depressive nature. Since the very timely appearance of their team leader had significantly lighted the atmosphere.

Noticing her approach the group looked towards her in expectation.

"Sheppard has made it through surgery and is resting comfortably." Teyla answered their silent question. "Elizabeth has requested one of us to sit with him."

Rodney snorted. "You mean like we do every time he gets hurt."

"Yes, Rodney. Now I was going to go right now, if you two would like to join me and then take Torren to nurse Kendra for me, she has agreed to watch him through my shift." Teyla said, running her hands through her son's dark curls.

The men nodded and stood to follow her, Rodney grabbing a pudding cup before they left.

SGASGASGASGASGASGASGASGASGA

Carson hid a smile as Ronon, Rodney, and Teyla, who was carrying little Torren, entered the infirmary. He didn't want to give them the idea they could tramp through his hospital anytime they please, though they seemed to have that opinion anyway.

"And what do you think you all are doing?" He asked, setting a stack of paperwork on a nearby counter before approaching them.

"Seeing Sheppard, of course. What do you think we're doing?" Rodney snapped in a very McKayish fashion, craning his neck around to look at the curtain surrounding his C.O.'s bed. "Like always."

"Like always as in one at a time." The doctor replied. "I can't have all you breathing over him like a pack of wolves. The lad's immune system is severely depressed and he already has quite the fever, no need to make it worse."

"We're not gonna go sneezing on him." McKay said, even as Ronon sniffed slightly.

"That is fine, Doctor." Teyla cut in. "Will you allow one of us to sit with him through the night?"

"Aye, lass that would be acceptable."

Teyla nodded before turning to hand Torren to Rodney, who fumbled for a moment before he settled the small child on his hip, his face clearly showing his discomfort. "Take him to Kendra, I will take the first watch."

**So, short. I know but I wanted to get you guys something for a little while. Let me know what you thought. **


	5. Chapter 5

**Alright, well first off while writing the last chapter I realized that I wrote Weir and Torren, I didn't even think about it. :) So this is an AU story where Weir never left. Carson is still a clone and I'm just not going to write any Keller. I might mention her but I'm not sure yet. **

**Anyways just a moment of realization, so back to the story.  
**

Teyla stifled a yawn, her neck craned sideways on the hard plastic chair. Sheppard had not moved through the night. He was taking longer to wake than was expected but the doctor had assured her that there was nothing to be concerned with. The Athosian's face fell grim as she looked over her beaten C.O. and friend. Bruises covering his tanned skin along with red, scattered bumps of various size. They would itch and burn long after the bruises faded. While this was all greatly upsetting what truly made Teyla's stomach turn were the tears now carefully stitched along his cheeks. Her imagination ran through any of the possible ways that wounds like that could be acquired, each on growing more horrifying than the next.

She sighed, glancing at the clock across the room. Five minutes until the end of her shift and she would be relieved by Ronon. It had taken a while for her to learn and adjust to the Earth's way of telling time, having been used to simply glancing into the sky. It had taken Ronon even longer to adjust, or at least he had claimed it had, using the excuse whenever running late to meetings or mission debriefings.

"How's he doing?" Ronon's gruff voice rumbled behind her, she having not noticed his soft footsteps.

"He has yet to wake but Dr. Beckett believes he will make a full recovery." She replied as she stood, anxious to get back to her own bed. "He would like you to contact him immediately if there are any changes."

Ronon nodded without really hearing her, his eyes following the steady moved of John's chest instead. "I know the routine."

"I have no doubt there." Teyla smirked. "We have all been in this situation far too often."

Ronon's lip curled upward as well. "And it's always him."

"I believe Sheppard would consider himself neglecting his duty if he did not give Dr. Beckett something to fix every other week. It could almost be considered a hobby of his." Teyla nodded before placing a hand on Ronon's arm. "Now, I am off to bed. Good night, Ronon."

"Night." Ronon mumbled, sitting down in the chair and propping his feet on the edge of the hospital bed.

SGASGASGASGA

Sheppard's lip twitched as he fought his way to wakefulness, most people described a thick fog muddling their brain but John instead found himself pushing through a deep sludge. Awareness slowly crept up on him, he could feel warm blankets surrounding him and hear the consistent, steady beat of machinery. He was back in Atlantis, safe with friends. John was nearly giggling with joy at the mere thought of being home. He didn't have to face the storms anymore, no bugs, no beatings. Life was looking promising again. Everything was right again, except something was missing. It only took a few moments for Sheppard to figure it out.

The comforting warmth against his thigh he had grown to expect was missing. Concern made his heart rate spike, increasing the rhythm of the heart monitor. This drew the attention of Rodney, who was sitting next to the bed, typing feverishly away at the computer perched precariously on his lap.

One of the newbie scientists, straight off the Dedalus had gotten cocky, attempting to reprogram the jumpers to increase their shielding which had, unsurprisingly, not ended well.

As it was, Rodney was now trying to reverse whatever the idiot had done, seeing as the hatches were opening and closing on their own along with the invisibility cloaks.

McKay had been working on the problem for hours now but the solution had yet to present itself. He had nearly jumped out of his seat when one of the machines screamed suddenly.

"What the?" Rodney mumbled as he looked toward Sheppard. "Sheppard? Sheppard, you done being dead to the world?"

"M'kay?" John groaned, barely moving his cracked lips, small stitches tugging gently at his cheek skin.

"Wha' day 's.."

"Thursday, you were gone almost seven days." He said, before patting the man on the shoulder. "I'll go and get Carson."

Sheppard shook his head and grumbled. "D'n need h'm, jus need Gr'v..r." He was clearly fighting sleep and losing by the sound of it.

"Who? Who do you need?" McKay pushed him, shaking the man's shoulder gently but the Colonel was already out, sleeping peacefully once again.

"Rodney? Did he wake?" Carson asked in a soft voice. He had been making his afternoon rounds when he noticed that the scientist had moved from his usual position, hunched over his computer.

"Yeah, only briefly. Mumbled something about a 'governor' or something." He answered, running a hand through his thinning hair.

"How was he?" The doctor pushed. "Did he seem in pain?"

McKay smirked. "It's Sheppard. He never tells you if anything hurts. No, he just seemed tired."

Carson smiled, writing a few notes in the patient's chart.

"The lad wouldn't be himself if he simply told us outright." Rodney had trouble even picturing Sheppard, sitting in his bed, whining that his shoulder hurt or that the pudding was too warm. "Just let me know if he wakes again, will you?" The Scott's man stated as he moved towards the doorway, heading down to the isolation ward to check on his other patient.

SGASGASGASGA

Carson grimaced as he stepped into the circular room. It only took the quiet hiss of the doorway opening to set the canine growling. He was cowered in the corner once again, behind the small bed they had provided him with.

The doctor was carrying a tray which held a few pill bottles and a two bowls: one of food and the second of water. Beckett never claimed to be a veterinarian. As it was he was treating the collie as best he knew how. The poor animal had a severe infection raging through his body, a large abscess just underneath his eye bearing the brunt of it. Thankfully there were no signs that it had spread to the blood stream so the Doctor was treating him with a broad spectrum antibiotic.

Hoping to put him at ease, Carson went about his duties without paying the collie any mind. Due to the distrusting nature of the patient, he had decided he would be the only contact he got for the time being and while that meant he would treat and care for the canine it also laid the duties of picking up afterwards on him as well.

Carefully, with his back turned, he formed small meat balls with the processed meat and vegetable mixture the cooks had rigged up before concealing the multiple pills within. Hopefully this collie wasn't the type to figure it out, Carson wasn't looking forward to even attempt getting the medication into him if he did.

The entire process was completed in silence so as not to increase the collie's anxiety with needless noise. Carson slowly turned to watch the patient out of the corner of his eye, carefully counting respirations. He expected them to be high but as long as they did not appeared difficult Beckett was happy. The collie was healing decently and he was content with the progress.

"Have a good meal, lad." Beckett whispered softly before leaving once again. He had hoped to have earned a bit more trust by this point but the poor creature's abuse ran deep. Now if he would learn to trust, only time would tell and they would need patience, lots of patience.

SGASGASGASGA

Sheppard did not wake again until late that early that evening, far more lucid and aware than before. The first question he uttered was simple. "My team?" which once securing the fact that they had befallen no harm, his next question was stated with the same level of concern as the previous one: "Where's Grover?"

This had confused them all for a few minutes, Rondey trying to process why the Colonel was asking about a certain furry blue monster. Perhaps there had been brain damage that Beckett and his voodoo science had not detected. It was Carson who made the connection first.

"You mean your furry companion, don't you lad?"

"Yeah," Sheppard mumbled, slightly drowsy with the pain meds in his system. "Is he okay?"

"Aye, lad. Grover is fine, no need to worry bout him." The doctor reassured him, placing a hand gently on his shoulder.

"I want to see him."

"That would not be very wise at the moment, Colonel, and I can not allow it."

Sheppard looked up at the Scot with a hurt and confused expression but Rodney was the one to voice the question. "Why not? The mutt obviously likes him, or it wouldn't have protected him in the first place."

Carson shook his head. "I am not concerned about the dog attacking him but Grover has a high level infection and the Colonel himself is battling with some nasty bugs. Separating them will alow them both to heal quicker, at least until the fever has decreased." He threw in when John was about to argue. "Don't worry lad, you're temperature has dropped a few degree since yesterday, and I can see no reason for it not to continue as long as you follow orders."

"Can you give me a day that I can see him?" Sheppard asked, overjoyed with the fact that Grover was safe on Atlantis. After everything, they had made it back in one piece, relatively.

"All right lad. Let's say by Sunday, if your fever is down by six degrees and you are making progress you may see him." Beckett promised, with John nodding in agreement.

Stepping forward, Rodney was about to jump in and bombard Sheppard with questions as the doctor walked away but the Colonel was already nestled into his blankets, drifting to sleep under the effects of the drugs added to his I.V line by a very crafty Scots man.

**Well the dog has a name. It's actually the name of one of Joe Flanigan's dogs (he had three) and was suggested by Joaniexjony. Thanks again! **

**Please let me know what you think and if there's anything you might like to see happen. I'm open to suggestions. :)  
**


	6. Chapter 6

**I do not see how you people can post everyday, it's a struggle for me to post every other day. :) I guess I just don't have as good a handle on my life as the rest of you. **

**Well I hope you like this chapter.  
**

Sunday rolled around far quicker than Carson had anticipated but to John it had seemed to take forever to come. He had been on his best behavior, trying not to induce the wrath of his physician. He hadn't complained about taking his meds, answered all their questions, vague and to the point answers only, of course. The Colonel hadn't even pushed to be released early, like he normally would. He desperately wanted to see Grover, to make sure he was okay. It wasn't that he didn't trust everyone here to take good care of him but the mutt had saved his life, after all.

John could nearly contain his excitement as he waited for Beckett to give him the go ahead. The doctor had not mentioned Grover at all that day but a wheelchair had been tucked into the corner of the room, ready for his departure, so John knew he hadn't forgotten. So here he lay there, trying to find something to distract himself until the time came.

While Sheppard was anxiously awaiting the visit, Carson however was not. He was nervous; for both his patients. There was no way to predict how either of them would react to the stress and emotion of the situation. Sheppard's blood pressure had been slightly raised since he awoke and his fever was still present, if low. Grover, as he had now learned was his name, was really in no better shape. The poor canine was healing slowly due to his environment. The consistent fear and stress was not helping him at all. The one positive improvement was that Beckett had finally seemed to earn a bit of trust. Grover no longer cowered in the corner but seemed to grow curious about everything, still keeping a wary eye and a fair distance between them. It wasn't much but it was something.

"Hey, Sheppard." Carson barely looked up as Rodney walked into the infirmary and up to the Colonel's bed. "You up for a game of checkers?"

"Yeah, I guess." Sheppard agreed, even as McKay set the chess box on the table, rather heavily. "But, I want white."

The scientist groaned, setting up the chess pieces. "Fine."

Beckett waited until their game was done before walking up to them, pushing the wheelchair in front of him. He could see the light spark in John's eyes when he noticed his approach.

"We ready, doc?"

"Aye, Colonel." Beckett answered him. "Now, let's get you in and we'll go for a visit."

"Aw, doc, can't I walk?"

"No chance, lad." The Scot had learned a while ago that it was easier at times to simply put his foot down instead of trying to explain himself. "Now, hop in."

It could not be said that Sheppard hopped in but never the less he did make it into the chair, with only a small amount of help from Rodney. His right arm was completely out of commission and would be for awhile, encased in thick bandages to prevent it from moving.

He could not help but smile as he was wheeled down the corridor leading to the isolation chamber but his grin faltered when instead of pushing him into the room, Carson brought him into the observation deck.

"What's up, Doc?" He asked, fearful that Beckett had changed his mind. "I thought I was going in?"

"Aye, you will, lad." He answered as he parked the Colonel by the window, who took the opportunity to look out into the room below. "I'm just gonna check you over once more just to be sure."

Sheppard barely heard Carson's statement, instead his eyes searching the expanse of the room for his companion. His sharp eyes finally noticed a lump of fur curled in the midst of blankets, tucked in the corner. A large wave of relief settled over John at the sight of Grover safe and sound, while his surprise became apparent when he processed the color his friend now was. No longer was he the scruffy black creature he had known but a sparkling clean black and white canine.

"Alright lad." Beckett muttered as he set his stethoscope back around his neck, breaking the Colonel from his thoughts. "Now let me just go over a few guidelines then we'll go down."

The doctor waited until Sheppard met his eyes before continuing. "First off, I will not have you doing anything to compromise your health. If you, or him, get too overstimulated it could set both of your recoveries back and I don't feel like fixing you up again." He warned.

"You don;t need to worry, Doc. I'll be fine." John reassured him.

"Of course, I do. You, lad, are a magnetic for medical mysteries. Now, second, you still have a lingering infection in your lungs, that means you need to keep contact to a minimum.."

"I got it, Carson, how about we go in now and you stop your worrying." Sheppard interrupted him, sounding like an anxious child on Christmas morning.

"Aye, lad." Beckett acquiesced, stepping behind the Colonel once again.

Anxiousness fluttered in John's stomach as the entered the the isolation chamber, the hiss of the doorway waking Grover.

"Hey, boy." Sheppard's voice cracked slightly as the canine looked up. It only seemed to take seconds for Grover to cross the floor, causing Carson to smile at the sight. It was the first time he had seen the mutt wag his tail, or what was left of it. As it was the stub was wiggling at a furious pace.

A pair of small paws planted themselves firmly on John's legs while a cold, wet nose was pushed into his face, sniffing every inch of him as if to make sure he was okay.

"I'm fine, Grover." Sheppard answered the dog.

A lop-sided grin broke out across John's lips, it's obvious joy only comparable to the smile seen during flight. The calloused yet gentle fingers of his left hand combed through the soft, medium length hair. While there was a notable difference in Sheppard manner, there was a complete change in the canine. His muscles, having been tense at all times, were relaxed and the wary glint in his eyes was missing.

"Missed you, Grover." Carson overheard the Colonel murmur. "Didn't think we were gonna make it back there. Not after-"

Beckett slowly took a couple steps away from them and busied himself organizing one of the medical units, feeling as though he was eavesdropping on a very personal moment. Sheppard had only told them the basics of his imprisonment. He had not been asked any questions, not been given any food, though it had rained often enough to prevent dehydration, and his captors were only interested in capturing off-worlders to kill them slowly then send their bodies back as a warning to any others, much like they had with Clarke.

The doctor could not even fathom the pain that each day would bring, knowing you would only face hatred and torment until your strength failed, only to wake and start again.

"Don't worry." Beckett could still hear John's murmuring and the temptation to steal and quick glance was overpowering. Sheppard still had his hands slowly dragging through the mutt's fur, while Grover had his eyes trained on his friend, tongue rolling out one side of his mouth. "These are good people, they'll take care of you, I won't let them separate us."

Grover seemed to perk up at this, his ears raising slightly from their normally floppy position. Carson could only hope that they could find a way to allow the canine to stay. Such things would never be even considered on Earth but here on Atlantis there may be a chance. There were obviously medical advantages that came with having a dog on base. The therapeutic world had found a great many uses for the furry companions. Beckett had already noticed the physical changes in Sheppard. His complexion had improved, the pinched expression of pain was absent.

"Carson?" John's quiet whisper was barely heard by Beckett. The tone of voice as well as the fact that the Colonel had used his first name, which the lad rarely used, told him that his patient was going to ask him something that he was sure would not be allowed, but it was important enough for him to request.

"What is it, lad?"

Sheppard looked down, before making eye contact once again. "Can, um..can I stay here tonight? Or...or Grover stay with me?" His eyes had a surprisingly soft quality to them, one that Carson had never seen. Every possible reason not to allow it immediately began to scroll through the doctor's mind. Increased chance of infection being at the top of the list as well as the fact that they still were not sure how Grover would react to everyone.

John broke contact once again as Carson sighed.

"You said my fever was going down and the antibiotics have been doing their job." The tone was desperate, but not in a degrading way.

"Tell you what give it two more days, lad. We want to make sure you can fully recover before taking chances again." Beckett continued when John's face fell. "But you may come and visit for an hour of so each day. How's that sound?"

"Okay, I guess." Sheppard agreed slowly, nodding slightly before turning back towards Grover. "I'll see you tomorrow, buddy. Just be good and I'll be back soon."

Carson felt like quite a villain as he wheeled his human patient back out of the room, leaving a very confused canine behind them.

**I know we haven't had much whump yet, but it will come. I promise. Just have to let them heal before hand. :) please review and let me know how I did!**


	7. Chapter 7

**Hey! Well my sister and best friend came back from college, so with ten people in the house with me. I didn't have time to write much, but I hope you enjoy this little bit. **

Much to Carson's disappointment, the signs of improvement he had noticed in the Colonel faded almost immediately once they left the isolation chamber. His pinched expression of pain returned and while John attempted to hide it, his doctor had had too much experience not to notice the wrinkled forehead and slightly squinted eyes.

There was no argument from Sheppard as Carson helped him back into bed, quickly reattaching the IV line and injecting a dose of pain medication into the port.

"There you are, lad." He said, giving Sheppard a short pat on the shoulder. "Now, Ronon said he would be in after dinner so you rest up until then."

John gave him a small nod. "Thanks doc."

Beckett smiled as he turned to walk away. A quiet murmur from Sheppard, however, had him turning back around.

"He saved my life." John's voice was soft but thick a clear indication of the emotion he was hiding behind it.

"How so, lad?" Beckett asked, feeling slightly guilty even stating the question. The Colonel was obviously raw after being reunited with Grover but John had yet to talk about his experiences, pushing them deep down and locking them away instead.

"He..he chewed my ropes when the storm came. The men were scrambling around, trying to keep everything dry so they didn't notice him at first." Sheppard glanced down at his hands, fingers gently rubbing against the thick bandages over his left thigh. Carson's light blue eyes tracked his movements, knowing what hid underneath.

"The leader had been angry. He thought you would all leave when you couldn't find me and...and when you found Clarke. The statement was clearly loaded and though he did not expound with the details, that did not stop the memories from accosting the Colonel.

_Rambo was screaming again, his vocal cords fighting to be heard over the growing thunder. Yes, the Colonel had titled his captor Rambo, the main reason being he was in a jungle and the man did have an unfortunate resemblance to Sylvester Stallone plus a thick head of very dirty dreads. It hadn't been as far of a reach as some of his previous nicknames for the beings of the Pegasus galaxy. John was currently laying at the man's feet, barely conscious. His hands were strapped tightly in front of him while his ankles were tied firmly in place. There was no way for Sheppard to protect himself as the boots connected with his flesh. Each grunt and gasp was drowned by the increasing winds. _

"_Why won't your people leave?" Rambo yelled, driving his toe into John's back. _

"_Told you.." The Colonel mumbled between pained groans. "They won't-ugh...leave 'til they- find me."_

_Sheppard screamed as pressure was applied to the deep stab wound on his arm. "Then they will find you dead!" _

_John shook his head weakly. "Y-you saw my weap'ns...mmgh. Wha' they can do..they'll find yo-" The rain was now beginning to increase from the steady sprinkle until John was laying in an ever growing mud puddle. _

"_Like how they found us after we delivered your friend? John's captor growled, withdrawing a silver knife from his belt. A shiver ran down Sheppard's spine as a crack of lightening illuminated the blade for a split second. "I don't believe we have much to fear. If they have not found us yet, then they won't be able to find us after you're dead but I'm tired of these games. It's time to end this but don't worry, we'll do this nice and slow." _

_If the line had been in a movie, John would have rolled his eyes at the typical threat, but when directed towards him, the simple sentence did indeed stir fear in his gut. Bending down to rest on one knee, Rambo pulled the Colonel's head up by his dog tags. The small, but strong chain digging into the tender flesh on the back of his neck. "Why don't we get started?" _

_John gasped as the sharp point of the knife drew a long, thin gash along his cheek bone. The following few minutes were a blur of pain for John as the large, dirty hands slashed at any available skin. His blood was soon trickling down to mix with the mud. Rambo was proving true to his word, each cut was __shallow, still painful, but no where near life threatening. With each cut the storm around them grew in intensity, pouring sheets of rain down on them. _

_The bad weather seemed to feed Rambo's bad mood though what really seemed to upset him were his prisoner's lack of screams, encouraging him to seek out more creative ways to cause John pain. Smirking, the man placed the cool metal of the blade between the Colonel's fingers, a hand harshly wrapped around John's wrist to hold him in place. Sheppard gasped, though there was no pain, yet. He was remembering the phantom agony that had seared through him when the A.I device had made him hallucinate Kolya, who had proceeded to cut one of his hands off. It was a pain he never wanted to go through again, in his head or not. Clearly enjoying the fear in John's eyes, Rambo slowly cut into the webbing between each finger. _

"_Carek!" Much to Sheppard's relief one of Rambo's men ran up at the moment he was preparing to remove a finger. "Carek! The camp is flooding! We need to move to higher ground!" _

"_What do you mean, flooding? This clearing has never flooded before!" Rambo yelled, looking around him at the rising river. Growling at the man to get ready to move camp, Rambo turned back to Sheppard. An agonized scream broke from his split lips as the knife was plunged into his thigh, luckily missing the artery. _

"_Call it a parting gift." His captor hissed, twisting the blade slightly before pulling it back out. "We can't carry you out of here in this storm so I hope you can swim." _

_With a final chuckle at his own joke, the man walked towards the his men, who had quickly tore down camp and were now waiting on their leader. Sheppard watched them disappear into the trees before struggling to free himself from his bonds, but to no avail. The water was rising around him quickly, lapping at the edges of his face, the gentle threat of impeding doom. _

"_Grover?" He called into the storm, doubting he would be heard over the thunder. The canine had been shot earlier that day by the men, having gotten to close to the camp. "Grover? You there boy?" A small smile graced John's lips as he noticed two deep brown eyes staring at him from within nearby bushes and he barely heard a soft whimper emanating from the area. _

"_Hey boy, mind giving me a hand with these?" He asked, lifting his hands up in front of him. The ropes were far too tight for him to slip out of and there was nothing nearby to help break such thick rope either. Grover tentatively hobbled from the brush, keeping a close eye around him for the guerillas. His teeth gently worked at the rope surrounding the tender flesh of his friend's wrists, not wanting to cause more damage. Within a few minutes the bindings fell away and John quickly freed his feet was well. _

_He ripped a piece of fabric from his BDUs and wrapped it around his leg. _

"I would have drown if he had been there." John muttered, not making much sense to the doctor but as long as the Colonel was talking Carson was happy to listen. "You can't let Elizabeth send him away. He needs us." _An' you need him, don't you, lad? _Carson thought as John yawned.

"Why don't you get some rest. The faster you heal, the sooner you'll see the wee dog again." He suggested, even as Sheppard's eyes dropped closed.

**Please review! and let me know if there are any words missing or anything, I didn't much of a chance to proof read myself. **


	8. Chapter 8

**Well, this chapter was a battle to get out but it is here. I always end writing sections of the story before hand, whenever things inspire me, but the hard part is making them all fit in a plot and connecting the dots. but either way, this is it. hope you like it. **

The next few days passed like a blur for John, minutes turning slowly into hours with nothing of notable importance to remember it for. Sheppard had already watched the entire collection of movies Atlantis had to offer, flipped through every magazine they had, and had read War and Peace until he could not bear to read another chapter.

Teyla smiled as she walked into the infirmary, despite the wailing child she held in her arms. Torren had woken with a mild fever and while Teyla was not terribly worried, she would rather have him checked out just as a precautionary measure. Being a part of this expedition meant she could potentially carry any number of unknown pathogens home and while Atlantis had 'state-of-the-art' scrubbers, as Rodney had put it, she still insisted on taking steps further.

Torren's screams, understandably, drew the attention of the entire ward, including Carson, who was in the process of re-bandaging John's lacerated wrists.

"What's the matter with the little guy?" Sheppard asked, while Carson left his work to feel Torren's forehead.

"He has a fever and has not stopped crying." Teyla answered, handing the small child over to Dr. Beckett's waiting arms.

"Well then. Let's take a look at you, lad." Carson said in a cheerful voice. "Marie, will you finish up with the Colonel, here?"

The small nurse nodded, moving forward, giving John a small smile as she grabbed the gauze hanging from her patient's arm. Sheppard watched silently as Beckett carried Torren over to a nearby bed. Teyla stood behind her son, holding him still as Carson took his temperature as well as did the general poking and prodding that seemed to be a universal diagnostic tool no matter the healer's level of training.

The gentle hands of his mother trailed through Torren's hair, slowly coaxing his wails into whimpers.

The entire process only took a matter of minutes, after which Carson gave a small sigh while straightening up.

"Well, you have nothing to worry about, my dear." He said happily. "This little one is simply growing up. Cutting teeth is bound to increase his temperature and will make him a bit cranky."

John smirked as Teyla's cheeks turned a light shade of pink and she looked down at her son briefly. "I seem to have over reacted. I am sorry for taking up your time, Carson."

The doctor gave a hearty laugh, placing a hand on he shoulder. "All new moms are a wee bit overprotective of their children and I'm glad to see the wee tike anytime. Always boosts the moral round here to see someone so full of life."

Beckett tickled the young boy's rather pudgy belly, receiving a small giggle for his troubles. "I have some low strength pills you can give him for the pain if he gets really bad. I'll go grab you a few."

Teyla heaved the child back into her arms as the doctor walked away. Torren was a husky boy for his age, something he got from his grandfather.

"How are you feeling today, John?" The Athosian asked, leaning a hip against the mattress while Torren sat, perched, on the other.

"I'm fine. Can't seem to convince the infirmary dictator or there though." Sheppard said, nodding in Beckett's direction. Torren's teeth seemed to start giving him trouble again as he began to wail again.

"Shh, Torren." Teyla said in a whisper, rocking him back and forth while rubbing his head, which normally helped, but did not seem to be doing the trick this time.

"Here, let me try." Sheppard said, holding his good arm towards the baby while being careful not to tangle his IV lines. Soon, Torren was nestled in between the Colonel's arm and chest, while soft words were mumbled into his ear. The small blanket John had knitted was wrapped around the small body and Teyla was left to sit and watch as large brown eyes slowly dropped closed.

The Colonel looked truly parental, laying there with the small bundle in the crook of his arm. So much, in fact, that Teyla could not help but voice the question.

"John, have you ever considered having children?"

"Kids? Yeah, of course." He replied, a vacant look in his eyes as he stared down at Torren. "Always wanted them, but Air Force didn't really work into the plan. Then Nancy was too busy with her career and I was never there anyways." Again, Sheppard's gaze did not move. He was lost deep in thought, imagining what things would have been like if he had had the chance to have a family.

"Always wanted a lot. Four or so. It always seemed like a good number."

Teyla smiled, imagining four miniature Sheppards running around and the chaos that would ensue. "Perhaps someday, you will still have that chance."

"Maybe."

Each of them sat there in relative silence until Beckett returned. "Looks like you have your hands full there, lad." He stated, when he caught sight of the Colonel and Torren. "Now, Teyla. Give him one of these a night and it should help him sleep and in the morning if he gets a bit cranky."

"Thank you, Carson." Teyla smiled, taking the pills from him. "Now, I would allow you to hold him for longer but I am due to meet with Amelia in the gym-"

"I'll take care of him." John said, eagerly. "I'm not exactly doing anything and can take him off your hands for a bit."

Teyla was about to protest, suspecting that the doctor would not want Torren in the way if something were to happen but she was cut off by Carson. "I think that would be an excellent idea." He replied, having noticed the improvement in Sheppard's vitals when holding the child, much like had happened when he was around Grover. "If anything would happen I will be sure to contact you, lass."

"Very well." She said, slightly relieved to have an hour of silence for a change but feeling guilty leaving her child for John and Carson to care for. "Please call, if you need anything."

"Will do." John answered as she walked from the room.

It only took a matter of minutes for Sheppard to dose off as well, his body still fighting an uphill battle. Carson placed an extra blanket over the both of them and left them to their dreams, occasionally stealing a glance at the peaceful scene, that was until Dr. McKay entered the infirmary.

"Beckett!" The scientist's high-pitched voice broke through the silence, holding a small rag against his left palm. "Bleeding here!"

"Shh!" Carson snapped, turning around and quickly placing a finger on his lips while motioning towards the bed. Torren had not moved from his position but John did shift slightly before settling down again.

"Well, I'm bleeding out here." Rodney whispered harshly, struggling to pull himself up on an empty exam bed nearby. "It's not like he hasn't slept enough this week."

Not wanting to explain that he needed the sleep, once again, Carson sighed as he walked up to his newest patient. He gently took Rodney's hands into his own, turning it over and removing the fabric that was wrapped around it.

"Stop pulling away from me." He scolded as McKay hissed in anticipated pain. "So what happened to you? I didn't think you were working on anything dangerous this week?"

Rodney was, unsurprisingly, a common client of the infirmary. His hypochondriac tendencies had him in and out of the clinic for small things but just as often there were 'mishaps' with the multiple devices he was researching in his lab.

"Snot-nosed newbie decided to fire up one of the objects we pulled from Janus' secret lab. I went to grab it from him and the thing did this!" McKay grumbled. "And I still don't know what it is."

"You're gonna need some stitches." The doctor mumbled, walking to gather the supplies he needed.

"Ouch!" Rodney shreeched as the doctor began to fix him up. "Do you have some sort of numbing voodoo? What kind of doctor are you?"

"That was the numbing injection. You should be loosing feeling soon." Beckett replied, without looking up.

With the analgesic effects working, Rodney found himself looking around the room so as not to focus on his hand, his gaze falling onto Sheppard and Torren, still sleeping deeply. The small child was snoring slightly while John's eyes seemed to be reacting to something under his eyelids. Their hair was the same shade, and if Rodney had not known who the kid's real father was he would have sworn they were related, their hair standing on end in almost identical styles.

"So, first he's the dog whisperer and now he's the baby whisperer too?"

"You're just jealous the lad likes him more than you." Carson said. He was meticulously cleaning the wound so that he could stitch him properly.

"I did help with his birth. You think he would be a little appreciative." McKay further grumbled. "You didn't see Sheppard there to help."

"The lad had his hands full, I don't think he could have just dropped everything."

McKay nodded, reluctantly agreeing with the doctor.

"It's the first time the Colonel has slept this peacefully since he got back. He sleeps better when Grover's nearby, or apparently Torren, so it seems."

"The mutt? Why would it help to have him around?"

"You've never had a dog, have you, Rodney?" Carson asked, knowing that anyone who had owned a dog at one point or another would know why it helped.

"No, my mom thought they were too obnoxious and messy. Which I have to agree, they demand too much attention and are so needy." McKay replied. Beckett did not bother to point out that the scientist had just described himself.

"Well, lad you should be fine. Just keep an eye on it and we'll take the stitches out in five to seven days." Beckett said, finishing up his work and picking up his remaining supplies as Rodney slid off the bed, heading towards the door.

"Rodney?" Carson stopped him. "Would you mind coming to sit with the Colonel tonight after dinner? He's going to be wide awake by then and I'm sure he would appreciate the company."

Rodney nodded. "Sure thing, Colonel. Now if you don't mind, I've got to get back to my lab and fix whatever those imbeciles have destroyed while I was gone."

**Don't worry, there will be more john and grover in the next chapter and hopefully more whump. and please review! reviews are better than cookies. :P**


	9. Chapter 9

**Hey everyone. Sorry this update took awhile. Family emergencies came up and I couldn't get to my comp for a while. **

**So here's the next chapter, hope you like it.  
**

"Doc?" John's voice was soft, so as not to wake the still sleeping child beside him. He had just awoken himself and sleep was still tugging at the edges of his mind, demanding more.

"Yes, lad." Carson answered, walking up to the Colonel's side. Beckett had managed to make a decent dent in the never ending stacks of paperwork that consistently cluttered his desk. The rest of the day had gone slowly, Rodney being the last patient he had seen, which had given him plenty of time to work through the files while keeping a close eye on both Torren and John.

"Tomorrow will be two days and my temp is down. Do you think Grover can stay with me now? At least until we know what were gonna do with him?" Sheppard asked, shifting slightly to sit upright while flashing the doctor and cocky grin, hoping to further convince him.

Beckett smiled slightly. "I'm sure we can, lad, but that all depends on how well he behaves. Now, I typically would not allow an animal in the hospital but there are no teams scheduled off world this weekend so I'm not expecting any new patient's."

John nodded, the small smirk that only he could pull off tugging slightly on the stitches across his cheeks.

"How did he do?" Teyla's voice was soft as she walked up behind Beckett, making him startle slightly.

"Teyla, warn me next time." The doctor hissed.

The Athosian's giggle echoed slightly in the quiet room as she placed a small hand on his shoulder. "I am sorry, Carson. I did not mean to startle you."

"Kid slept since you left two hours ago." Sheppard answered her previous question. "Didn't get cranky once."

"Well, then he may just come and visit the two of you more often, if he slept that well." Teyla replied. Torren had immediately taken a fancy to John, not in the sense that he would never cry when in his arms, there having been plenty of times the Colonel had quickly handed the fussy baby back to his mother, but they had bonded. Torren seemed to find find a peace when around John, it was the same effect the small, blue blanket had on the child. Teyla suspected it was because the blanket still smelled like Sheppard, a subtle blend of coffee and aftershave. The object had, after all, been been present in his crib only a few days after his arrival, Sheppard having knitted it while recovering from the stab wound he had received in the building collapse.

"Well, I must go. Thank you again for everything."

Carson grunted as he took Torren from John, handing him over to his mother. "Now, lad. I asked Ronon to stop by in an hour or so to help move you to the iso room."

John's expression was slightly confused but happy as he looked up at the Scot.

"Thought we were waiting until tomorrow?" He asked, instantly kicking himself for reminding the doc.

Carson answered him after bidding goodbye to Teyla as she left, with Torren in her arms. "Your fever has lessened and you seem to be improving greatly, so while I shouldn't allow this, we'll move you in tonight. Wee Grover has been missing you something fierce, and he'll be wanting the company."

John smiled, and was about to say something but Beckett interrupted him. "Now, none of that is going to happen until we make sure nothing is amiss."

"Doc, I feel fine." Sheppard argued. Yes, he wanted to see Grover but he had been through the infirmary a time or two and knew Carson's limits. He just really hated all the poking and prodding that was associated with check-ups.

"You, lad, could be bleeding and unable to move on this floor and still insist you were fine. Now, hop off that table and we'll get you over to the scanner."

SGASGASGASGA

_A low, feral growl broke John's cracked lips as he fought the losing battle against the ropes encircling his wrists, which was muffled by the dirty rag tied around his head. He had awoken a good hour ago, secured upright to a large fallen log, set slightly outside the run down camp. A demanding headache was pounding between his temples as though his entire high school marching band were practicing within his skull, and they had never been very good. _

_Sheppard's captors had yet to notice that he was awake, something the Colonel was very grateful for. As it was the only men he saw were two prone figures lying, seemingly asleep, near a roaring fire pit. A blaze John would have loved to have been even a few feet closer to. The nights on this planet were not cold by most standards but when one was soaked to the bone and suffering from a concussion your body did not follow the normal logic. _

_The crack of a stick caught Sheppard's attention and he looked up to see two men appear around one of the poorly crafted huts, dragging a limp figure between them. All three were silhouetted by the fire light. _

_They were slow, struggling to move the dead weight between them before dropping the man in front of him, allowing him to see his fellow prisoner in detail. _

_Torn BDUs hung off bruised and broken flesh. Mud clung to nearly every inch of skin but through all of that Sheppard could make out the sharp features of Lt. Clarke. _

"_Hmph!" John grunted, an attempt to get the soldier's attention, momentarily forgetting about the gag. _

_Ruby droplets were slowly dripping from Clarke's lips but his light blue eyes were open, blinking slowly. _

"_C-col'nel?" The broken whisper was near a scream to John. The man's gaze quickly turned from confusion to pain as hands dragged him over next to Sheppard, where his hands were harshly secured behind him. That done, their captors left again, without a word. _

_Clarke gasped, trying to catch his breath before looking towards John. "Are- you a'righ, Col..?" The soldier wheezed. _

_John nodded, attempting to express his own questions despite the obvious obstacle._

"_I'm fine too." The Lieutenant answered, knowing his C.O well. He also knew Sheppard would be needing a briefer on their situation so he continued. "There are ten men in the camp but I've heard them talk about others further in the jungle. No obvious weak points or opportunities yet." The man paused slightly. "I'd ask you how the rescue was going but by the looks of it, not well." _

_All Sheppard could do was nod once again. Of course, being the sharp witted flyboy that he was, a sarcastic remark was instantly on the tip of his tongue, one he could not use at the moment. _

"_I have one trick up my sleeve though, sir." Clarke said with a smirk. "And that doesn't count folding my tongue into a flower, either." _

_Hazel eyes narrowed in exasperation but the amused spark was not lost on the Lieutenant. Although he was a 'simple marine', Clarke had Rodney's ability to ramble, making him one of the less popular soldiers on Atlantis but by no means unlikable. Marines were often men of action and few words but the Lieutenant broke that mold, but he was still a exceptional soldier. _

_Unlike Rodney and his rambling, Clarke understood when to quit and get to the point, so with a quick smirk he let out a low whistle. _

_A moment passed in silence with John staring bewildered at the man, before loud rustling in the foliage between them startled the Colonel. _

"Hey, you about ready to go?"

Ronon's low voice broke John from his thoughts as he sat in bed, attempting to file his report. Being a private man, writing about his experience without revealing more than he wanted was difficult. He didn't want people to treat him any different than usual and while the details were crystal clear in his mind what he had currently written was simple and to-the-point. The short sentences only hinting at the true horror underneath.

"Yeah, I can't wait to get out of this sterile prison, even if it means being stuck in another one." Sheppard answered as he closed the beige folder.

Ronon smirked before placing a hand on the Colonel's shoulder as the man attempting to stand. "Hang on. I'll go get Beckett and get your wheelchair."

John gave the Satedan a intense glare and muttered 'traitor' quietly under his breath as Ronon walked away. If it had been Ronon in this position, the man would have refused the chair, let alone the help, wanting to do it on his own if only to simply prove he still could. That type of thinking, however, was only applied to him and he insisted the Sheppard follow the doctor's requests to the letter, that was until he felt that Carson was being overprotective, which would happen eventually.

The Colonel only had to wait a few minutes before Ronon reappeared with Carson in tow, who was pushing a wheelchair in front of him.

"You still feeling up to this, lad?" The doctor did not truly expect John to change his mind, he knew the pilot better than that, but if the universe was going to be turned on end that day, Carson wanted to know about it.

"Never felt better, doc." John replied, swinging his legs over the side of the bed with a small grunt.

"I doubt that very much." Beckett mumbled under his breath as he pressed the wheel brake down on with his hand. "Now Ronon, help the Colonel in, if you would."

Sheppard was soon sitting in the chair, panting from excursion. He had, stubbornly, insisted on getting himself into the metal contraption, though still leaning heavily on Ronon's arm.

"Stubborn idiot." The Satedan hissed as John ran over his foot, trying to use his one good arm to move himself around. The large man grabbed the handles and began to push him towards the door, Carson following close behind after picking up a few of John's personal belongings from around the bed he had previously occupied.

The short walk to the isolation chamber was silent, none of them having anything of great importance to say. That peace was broken however the minute they cleared the threshold of the room holding Grover, his low growl emanating up to the high vaulted ceiling.

"Grover, dude. It's just us." John said, holding a hand out to the mutt, but his words did not seem to calm him.

"What's wrong with your dog, Sheppard?" Ronon mumbled from his position behind the Colonel.

"I have no clue." Grover had not growled since John had begun seeing him everyday, seeming to understand that no one here would harm him. "Grover, what's wrong?"

Trying to comfort his companion, the pilot leaned forward in the wheelchair. Unfortunately with the combination of the pain killers in his system and the slow pace that he was regaining his strength, John's balance was slightly off kilter and he began to take a nose dive forward. With Ronon's sharply honed reflexs, the man's large hands were immediately reaching out to stop the Colonel's inevitable nose dive.

It was at that moment that chaos broke out.

**Thanks again for all your patience. Please review but no flames please!**


	10. Chapter 10

**Finally got the chapter done! This chapter was hard for some reason and I can't really pin point it, so I hope you all like it well enough. **

**Anyways, here you all go!**

Grover's ears perked up as the only entrance to the chamber, where he was currently being held, hissed open. The noise would have sent adrenaline coursing through his veins only days before but after a while he had grown lax. No dangerous humans or creatures had appeared in the doorway, no obvious threats had entered. In truth, the canine was beginning to trust the humans he had come in contact with, which were few.

His friend made his own appearances occasionally, but unable to see the sun in his prison, Grover never knew when to expect him. The other human he saw more often, the one who smelled of mint and disinfectant, was also nice. He had yet to hurt Grover which meant a lot to a creature that's previous encounters with any humans could only be described as cruel.

The small amount of kindness Grover had received was slowly chipping away at the thick barriers the canine had constructed. So when the door opened instead of the fear that was normally present was replaced with anxiousness, which was a far cry from terror, accompanied by a small spark of excitement.

Stepping out from the thick pile of blankets, Grover gave a small shake to adjust his fur and bean to trot toward the door, wagging his small, still bandaged tail as his friend entered. His happiness was short lived, however, when he saw the man standing behind his friend.

_The laughter was loud and harsh as a sharp pain erupted in his side, eliciting a high pitched yelp that tore through the air which was quickly followed by a whimper as the Alpha leaned over him. _

_Long fur that resembled the vines in the jungle hung from the man's face, his lips bared to reveal his teeth in a threatening manner. Grover whined again as one of the black sticks that the pack carried was raised to come down hard on his back. He could hear his friend barking nearby, objecting to the canine's harsh treatment. The Alpha had cornered Grover against a stack of crates, giving him no possible escape routes. Another low growl broke from the man's lips as he glanced back at Grover's friend, his hands tied securely. _

_Grover knew his whimpers would not be heeded, he was the Alpha after all, but they came anyway, a desperate plea to anyone to save him. The man would never show weakness, that was why he was the alpha. He made the decisions, choose who ate when and what, if they survived. Grover had thought about finding another pack, but the jungle was dangerous and packs were rarely receptive to loners, seeing them as a threat. _

_A flinch ran through the canine as Alpha clicked the black stick in his hand. He had seen what that stick had done to men and his fellow animals. Stuck down by an unseen force that Grover did not know. His friend's barking increased in urgency, but the canine knew that there was no changing the Alpha's mind. _

_The loud crack echoed off the thick trees around them, silence following it, ignoring the cawing of a few startled bird. The pain started immediately but was muted by his raging adrenaline. Content he had reinstated his dominance, Alpha backed up a few steps, a strange sharp noise emanating from his throat. Seeing his opportunity to escape, Grover charged forward but fell as he placed weight on his hind leg. Sharp pain lanced through it, sending the muscles into spasms. Wanting above all else to run away, he swallowed the pain and managed to get back onto his paws with his leg tucked up tight against his body. Running with all his strength, the mutt managed to disappear into the underbrush. He did not get very far, hiding underneath a fallen log to lick his wounds. _

Needless to say, the sight of Alpha behind his friend was a shock to say the least, bringing a snarl to his lips. He had thought this place would be different, safe, but he should have known this pack would not accept him either. His friend seemed fine, talking to him softly and leaning forward to get closer to Grover. The canine saw Alpha's large hands moving to grab his friend, hurt him, and Grover would not allow that to happen, not again.

SGASGASGASGA

A loud bark echoed off the walls as glistening teeth dug into Ronon's palm, drawing blood. Understandably, the Satedan withdrew his hands allowing John to continue his nosedive without obstruction, grunting as he managed to take most of the pain on his right arm and shoulder in order to save his useless left one.

This all occurred within seconds, and Beckett and Ronon were left standing against the wall as Grover stood in front of Sheppard, teeth bared and the low growl still in his throat.

"Sheppard?" Ronon mumbled, the single word asking a multitude of questions while neither Carson or he moved an inch, blood slowly dripping from his hand.

There was a small groan from the Colonel before he answered, his sore body protesting the sudden drop. "I'm good." He moved to sit up slowly, turning so he was facing them and the canine. "Grover, stop, Grover."

John reached out a hand to touch the mutt. "Calm down and get over here." Even this simple reassurance had a large effect on Grover, who back up to sit next to the Colonel, his eyes never leaving Ronon.

"He...uh, the leader of the guerillas..um, had dreads." He said, giving a short explanation for Grover's reaction, cutting short when he noticed the small puddle of blood underneath Ronon. "Dude, your bleeding!"

"It's just a graze." The Satedan mumbled, even as Beckett, who had nearly wet himself during the event, grabbed the appendage to examine. In the past two weeks he had not yet seen Grover respond that violently, of no one had looked like his former captor or made much contact with the Colonel.

"You'll be needing stitches. Why don't you head back to the infirmary to get that patched up and I'll get John set up here." Carson instructed, wrapping the wound with a temporary bandage to stop the bleeding.

"Sounds good." Ronon grunted, heading back to the door but stopped when John called out to him.

"Hey, Ronon! I'm sorry."

Ronon peeked around his shoulder, about to give the Colonel a sarcastic comment but was stopped by the guilt he saw on John's face.  
The man had a protector's heart, that had been obvious to the Satedan the first moment he had seen him. McKay had often accused the man of a 'superhero' complex, mostly once the newest threat had been adverted and Sheppard was being patched up in the infirmary. Being a Specialist in the Satedan military, Ronon had obviously observed Sheppard and Teyla for a while, before he had captured them. His stance had been of one of authority, prepared for action. Walking ahead of his team he was setting himself between the highly possible dangers, willing to be the one hurt or captured. John had proven that again and again since he was the one always in trouble, for the most part.

So upon seeing the concern on John's face, Ronon bit his tongue.

"It's no big deal, Sheppard. Really." With that said, he turned again and disappeared through the opening.

Sheppard's gaze remained on the now closed door for a few seconds until Beckett broke the silence. "Well lad, let's get you set up." He said as he placed John's laptop and other personal items on the bedside table.

"Sure thing, doc." Sheppard answered even as Carson helped him to his feet, hissing as the new bruises made themselves known. Having learned to trust the doctor, Grover moved out of the way and trotted slowly beside them as they made their way to the bed, tongue wagging happily once again as he believed the danger to be dodged once again.

"And, we'll take a look at those."

John sighed in dread more than pain as he managed to pull his way up onto the bed with the Scot's help.

SGASGASGASGA

"_We'll do this nice and slow." _

Sheppard gasped awake, sweat all but pouring off his overheated skin. Heart beating erratically, he place his palm across his chest half expecting to feel the muscle jutting from his skin with each powerful beat. Firmly wedged beside John on the small bed, Grover lifted his head suddenly and looked up at his friend with concern filled expression.

"I'm alright, boy. Just a nightmare." The Colonel sighed, scratching behind the dog's right ear. Grover did not seem to believe him, keeping a close eye on him until John relaxed back into his pillow before laying his head back along the man's thigh.

Wincing as he rose the arm that was not currently bandaged to the point of uselessness, John reached for the cup on the bed table. The good meds were nearly out of his system. He knew he should tell Carson, and would in a few minutes but for now John was simply enjoying the silence.

There had been no peace in the camp, quiet only when he was unconscious. The men always yelling and the constant clatter of weapons discharging nearby...and laughing. Cruel, vindictive laughter as they tormented him or Clarke.

They never gave you break. No matter the time or how tired you were. One was always nearby, watching and waiting for your guard to drop or you eyes to droop. Peace was only found when unconscious, where they could not wake you for further torture.

**Well, that's it. Please let me know if you liked it. :D**


	11. Chapter 11

**Well, when writing this I thought it was going to be one of the longer chapters but it's actually one of the shorter ones. Oh well. Hope you like it anyway. **

Ronon kept what he considered a normal pace, one that would have most people jogging along side him, as he walked down the corridor. The bandage was still wound tightly around his hand, slowly turning a dark brown as the bite continued to bleed. It was throbbing in time with his heart but Ronon would not admit it easily. Even after 'settling in' with the Atlantis expedition, Ronon was reluctant to show his pain readily. Pain was weakness and a runner could not allow himself to have weakness. He had quickly fell into the habit of hiding his pain from other people in order to convince himself that it did not matter.

In that way, the runner could relate with the canine. He had seen the pained way Grover had walked only to hide it as the group entered, his stiff movements giving him away. Though he was understandably frustrated, Ronon had already forgiven Grover.

"Ronon, what happened?" Elizabeth's voice took the Satedan by surprise as he entered the infirmary. SGA-4 had returned from a rather nasty run in with some unpleasant natives and were all being treated with various injuries, none of which were life threatening, thankfully. Weir had come down to check on them as well as Nurse Bennett if she would translate her latest report for her, the woman had horrible penmanship.

"Oh, uh. Grover and me don't get along very well, yet." Ronon mumbled as a nurse steered him over to an exam table.

"How did this happen?" Weir pushed, concern for him as well as anyone else in contact with the canine. "I was assured he was not a danger."

Dex replied quickly, not wanting to get Grover in trouble. He also wasn't sure if Sheppard would ever forgive him if he was the one to get the mutt locked away for good or worse sent off world. "He's not. He was just trying to protect Sheppard."

"And why did he need to protect Colonel Sheppard?" She asked, folding her arms across her chest. Her stern expression softening when a hiss escaped Ronon's lips when the nurse began to clean out the bite wound.

The large man sighed before beginning to regale the entire tale to her.

SGASGASGASGA

Sheppard's teeth were bared as he attempted to raise his arm, small blue ball in hand. The muscles were shaking from the strain.

A few days had passed since the incident with Ronon and after long and tireless attempts Ronon, Carson, and John had managed to convince Elizabeth that Grover was not a threat. They had held a meet and greet with Elizabeth and Grover, as well as including Teyla, which had gone splendidly. The canine did not have the intense of fear of women that he had with men. He had rarely encountered any females in his life and the few he had met had never harmed him. With this on their side, Teyla and Elixabeth were soon rolling on the floor in a very undignified manner, playing with Grover.

The Colonel could not have hoped for a better result and had been slightly encouraged for a small while that day.

Now however, he let out a low growl as his arm gave way, the sphere rolling across the chamber floor.

"Patience, lad." Carson stated calmly, standing up to retrieve the object of John's defeat.

"This is taking too long." Sheppard grumbled.

"Ye had the muscles in your arm severed, lad. Not simply torn. I sutured them back together but it will take longer to heal than normal." Carson handed the ball back to the Colonel. "Now let try again."

Slowly, John attempted to raise his arm at the elbow, quivering with the exertion.

_Sheppard gasped, staring at the knife handle now embedded in his flesh, just below his shoulder joint. Blood was sluggishly seeping from around the knife. The blade had passed through his arm burying deep into the large fallen log he was leaning against. _

_ He had no way to remove it, hands tied firmly behind his back. The slightest of movements sent shock waves of agony through his body. That was how Sheppard spent the entire night, shaking from blood loss and pain. _

SGASGASGASGA

Rodney sighed as he stopped in the isolation doorway, watching as a small ball roll across his path before meeting the wall. Sheppard had been at it for near an hour, Beckett having given up convincing him to rest. The scientist could almost see tears of frustration in the man's eyes as he tracked the ball's course away from him.

"Would you mind grabbing that for me, Rodney?" John asked, motioning with his good hand.

McKay was about to comply when he received a very pointed glare from the good doctor.

"I would but I don't think you're the one in charge here and the Scot's got big needles."

"Traitor." Sheppard mumbled, before looking down at Grover who was curled up on a towel, under the bed. "Would you mind, buddy?"

McKay watched as the dog trotted over, picking up the blue sphere before returning to his master.

"Alright Sheppard, this is ridiculous." McKay snapped as the ball fell from the Colonel's grasp once again. "You're just gonna slow your healing if you don't give yourself a break."

"I tried to tell him.." Carson mumbled from his desk a few feet away.

Grover moved to retrieve the ball once again but Rodney was also moving towards it.

"You know what, no." McKay said, reaching to grab it just as the canine did. Carson's warning to stop came fractions too late as a sharp warning back made the scientist freeze in place.

Rodney stumbled back as Grover retrieved the ball.

"I could have told you I already tried that." Carson stated calmly as the mutt trotted over to John and dropped the ball back into his lap. McKay did not reply to the doctor, simply looking from Grover and the Colonel to Beckett. Soon he settled to simply stare at Sheppard who's own gaze was nearly burning through the small, round object in his hand, not even attempting to form a fist around it. As usual, Rodney had a sharp retort on his tongue but found that he could not force it from his lips when he saw the dark shadow in the Colonel's usually bright eyes.

"Just leave the lad to his thoughts for a wee bit." Carson said softly, gently tugging McKay away from the bed.

Strangely enough, Rodney took the Scot's advice and followed him over to the other side of the room, speaking in a soft voice. "Teyla said he was depressed." He said, glancing back to John, quickly taking note of the dark circles under the man's eyes and his pale complexion.

"Aye, lad." Carson nodded while continuing his work in a feeble attempt to hide their conversation from the Colonel since he had completed most everything he could do for the moment. It was a well known fact that Sheppard hated being the subject of pity and he was also known to have a very keen ear, so Beckett attempted to lower his voice even further. "Something is troubling him but he has yet to confide in anyone."

McKay shifted from one foot to the other as the doctor said this. He wasn't any good at talking to people, especially about feelings and that kind of crap. Sure, he had managed it with John before and would gladly do it again but Teyla was so much better at all that than him.

"Now, I don't think it would be a good idea right this second, so you can quit your fretting for the time being, Rodney." Carson said as he turned and placed a hand on the man's shoulder, reading McKay like an open book.

"I believe the best thing for now is to let the lad rest."

Looking over his shoulder, Rodney could even now see the Colonel's head slowly falling back onto his pillow. Grover was curled into a small ball under the bed while keeping a close eye on Carson and him.

**Please review, let me know if you would like to see anything in particular or if I should even continue!**


	12. Chapter 12

The next few days passed slowly for all parties. Strangely enough, the off-world teams had not run into a single hitch and the scientists had not had (or caused) a single mishap, leaving everyone to bask in the unusual peace. This had also cleared a great deal of time for Atlantis' flag team plenty of time to visit their healing C.O, with Rodney balancing a few projects on the side of course.

A few quiet days also gave John a chance to heal and build up his strength. According to Carson he was not yet recovered enough to walk on his own, so John was confined to a wheelchair but allowed to make short visits with Grover to the East balcony. Sheppard had, of course, fought tooth and nail with the doctor but had backed down rather quickly when threatened to have his privileges revoked, much like the scolding one gives to a small child.

So here he sat, looking over the calm waves of the ocean. The sky was a deep blue above him but if John were to peer out toward the horizon in front of him, he could just make out a dark storm forming a fair distance away, the occasional lightening strike illuminating the near black clouds. Rodney had mentioned the upcoming tempest earlier that day but had failed to notice the pale pallor Sheppard had taken which only increased as McKay continued to ramble on about wind speeds and shield integrity.

The hiss of hydraulics and soft footsteps broke John from his thoughts.

He smiled as Teyla walked through the balcony doors, a small tray in her hands. The small, recently un-bandaged stub of Grover's tail began to wag furiously when he saw her and he left his self assigned spot next to John's feet to greet the Athosian.

"I was told I would find you out here." Teyla laughed as the normally well behaved pet jumped up on her.

"Grover! Down!" Sheppard scolded, to which the canine quickly obeyed and trotted back over to his newly adopted master.

Her smile widening, Teyla sat the tray down on the man's lap, revealing a small lunch. "Carson sent this since he knew there was little chance of getting you back into the infirmary for a meal."

Sheppard shrugged, not at all bothered that they knew him so well, as he began to pick at his food. The Athosian knelt beside the wheelchair, her fingers idly weaving through soft fur. Grover had grown very accustomed to the attentions of the Atlantians even after the few short days. He no longer hid or growled and while still skittish around most men given time he warmed up to those who gave any effort to befriend him. The only exception was Ronon. The man's tall stature and dark dreads mirrored to closely to Alpha for Grover to get passed easily.

"May I ask you something, John?" Teyla asked, slightly hesitantly for the normally self-assured woman.

Again Sheppard shrugged, it was becoming an answer he used quite frequently in the last few weeks.

Teyla took it to mean yes and continued to ask. "Some of the others and I have noticed the heavy bags under your eyes and your reluctance to sleep. Is there a reason you do not wish to rest? You know you can tell me anything."

_Sheppard grimaced as thunder cracked over his head seconds before the rain began to pour down in a soaking torrent. Having been in a great many jungles throughout his military career, whether they be on Earth or in the Pegasus galaxy, John had created a list of every reason he hated them. Sudden rain storms that gave no warning were definitely at the top of the list, next to endless bugs and the inescapable humid heat. _

_As it was, Sheppard was quickly drenched, his hair firmly plastered to his head and his black t-shirt clinging to his chest, reigniting the ache of each laceration. The gag in his mouth soaked up the water readily and while he had indeed been yearning for a drink for days, he soon had to choose between sucking the refreshing water from the fabric or continuing to breathe since his broken nose was too swollen to be of any help. Within minutes, he found himself fighting for air, choking on the water he inhaled with each attempt. _

_Dark tendrils were slowing creeping into Sheppard's vision from the lack of oxygen when he heard the squelch of boots as they stopped in front of him slightly before a low chuckle. _

"_I've seen a dozen men die in such down-pours." The man's gruff voice had a barely noticeable slur. "We'll see how well you do." _

_Never one to take anything lying down and also never having the common sense to stay on your captors 'good-side', John responding with his best glare, trying his hardest to put a cocky air behind it as well as a challenge. _

"_Think you can take it, huh?" John's torturer quickly rose to bait. _

_John gave a slight nod before the side of his head erupted in pain, making him groan through the gag. _

"_I know the hardest thing is to keep breathing through these nights, so we'll see how you take it with a concussion as well." The man nearly giggled as he said this, pointing the now shattered neck of his glass bottle at his prisoner. He dropped it near his feet before stumbling away. _

_The urge to shake off the waves of dizziness now accosting his brain was great, but the Colonel knew from experience that it only aided in intensifying the effects. Shards of the broken bottle now lay all around him and he could feel his own warm blood seeping down his neck, confirming that, along with his scalp, his ear had been torn in multiple places. _

_John grimaced as he contemplated the night to come. He could not allow himself to sleep. If he were to he would suffocate for sure, but he could already feel the concussion pulling, making him drowsy. It was going to be a long, miserable night. _

Sheppard hesitated for just a moment before he smiled and looked up at Teyla. "I just don't like to miss out on anything."

SGASGASGASGA

"Well, lad." Beckett said as he walked over to the bed which John was currently reclined on, looking as nonchalant as he could while he waited for the doc to release him. The Colonel was more than anxious to get back into his own room since he no longer needed to be hooked up to any IV lines or monitored throughout the night any longer. Along with the urge for freedom the upcoming storm was making him uneasy. He longed to be in his own environment,where could control the temperature, humidity, and lighting. To know that he was in complete control of the weather in one area. While this may have seemed like a trivial detail, to John it was a way to control something for a short time.

Sheppard's career had had him captured and held prisoner more times than the man could count and he had decided long ago that the worst part of each imprisonment was the loss of choice. He would sleep only when they slept, was dragged where ever his captors fancied, and eaten only what they would give him and that was only if they gave him anything at all.

"I can't think of a single reason to keep you here but I would feel better if you did." Beckett said, pushing the wheelchair in front of him. "Now, I want you to stay in this thing the whole time. None of this 'superman' business trying to walk yet. You are still very weak and need rest."

John groaned slightly as the Scot helped him into the chair. "Don't worry doc, even I know I won't be jumping any buildings any time soon."

"Teyla will help you get settled-" Beckett began to state when he was interrupted by Elizabeth who had just walked through the door.

"Actually, that would be me." She said, placing a hand on John's shoulder. "Teyla needed to stay with a very cranky Torren so she asked me if I could help with the move."

Sheppard smirked slightly, as long as he was getting out of there he didn't really care if bigfoot was his guide. "Sounds good to me."

"Alright, now remember lad. I have each pill clearly labeled and someone will of course be there to help you with Grover's." The poor mutt was on his regime of drugs, the numbers nearly equaling the Colonel's.

"Yes, mother. I've got it. Don't worry." Sheppard replied in an exasperated voice while a light-hearted grin cracked his lips, telling the doctor he didn't mean the harsh tone.

"I'll make sure we've got everything, Carson." Weir assured him as she pushed the wheelchair in front of her, pausing to make sure Grover was following them.

While the IOA did not like it, Grover was to stay on Atlantis as a therapy dog. Elizabeth had convinced them of the canine's value during a fairly long conference throughout a scheduled check in. Though slightly underhanded for her, she had left out Grover's own psychological issues while pointing out the multiple benefits that a therapy dog would bring to the base. The 'straw that broke the camels back' however was a short video of Teyla and Torren interacting with the mutt and the smiles of each patient in the infirmary that day.

It did not take long for the group to reach the Colonel's quarters and Weir quickly had him situated on the bed and everything he might possibly ever want or need within arms reach.

"Now, are you sure there isn't anything else? Do you need anything to eat?" She asked while scanning the bed side table which already held a pitcher of water and cup, his laptop, gameboy, his book: War and Peace (in which he had barely made a dent), and all his pills.

"No, you have everything, now would you go? You've got better things to do besides babysit me all day." He said. "I promise to call Carson if anything changes and I'll call you or someone if I need anything. Happy?"

Elizabeth smirked and the Colonel raised his eyebrows at her. "I guess. Someone will be back in a little while." She said before slipping out the door.

Sheppard lay there for a nearly forty-five minutes simply drifting in and out of sleep with Grover pressed close to his thigh. The sleep was not peaceful, John shifting constantly and occasionally mumbling. The Colonel was shaken from his sleep when a loud crack of thunder echoed outside his window. Rain pour down in sheets from the sky until he could not see anything if it wasn't a foot in front of you.

John quickly willed the windows to tint entirely. The city responded immediately to his request, blocking out all view of the storm. While the sight was obscured the storm could still be heard. The thunder roared and the rain beat an uneven beat of the cities spires. Growing nervous, John attempted to distract himself.

_Rain fell gently outside the house, singular drops of water plummeting independently only to merge together in the black waters of the sea. The small summer home stood firm against the summer storm. Soft green eyes followed the rivulets as they formed long, narrow tracks on the window pane while small, pudgy hands attempted to catch them, stopped by the cool glass. Giggles erupted each time the capture was thwarted. Thunder rumbled in the distance, a low threatening growl warning all who heard it of the approaching storm. _

_Soft arms enveloped the small boy from behind, one hand running through messy black hair while tender lips pressed softly against the back of his head. _

It was then that the scene faded. The scene was one of John's earliest memories, the first storm he remembered. While he had been young, it still held some particularly strong emotions. Even with the raging storm outside, he had been safe and warm, content and loved. It was the memory that had always allowed him to enjoy bad weather, watching the power surge through the sky. He had always found storms calming, often sitting for hours, which was an achievement in and of itself, observing as the dark clouds rolled in but that was before. John could not seem to find the tranquility he had once had as the lightening cracked overhead. They now made him anxious, unable to sit still, his subconscious not wishing to appear an easy target. John would not have admitted it out loud but he could not help but attribute pain to the storms. There had never been even a ray of sun throughout his imprisonment. He knew it was irrational, but he couldn't shake the feelings, or the memories. Grover had noticed his master's growing unease and was now sitting next to John, ears pricked and was nuzzling into the man's arm, trying to impart some comfort.

"Thanks buddy," John mumbled but his eyes never left the black window.

**There you all are, wanted to get you guys a chapter before Christmas and I hope you all liked it. Now a great present would be reviews, do you think? **

**Everyone please be safe and have a great holiday. **


	13. Chapter 13

**Sorry it took a bit longer everyone. The Holidays get pretty busy at my house, but anyways hope you like this chapter. **

Thunder roared outside Sheppard's window pane when Teyla appeared a few hours later, just in time for his multiple medications. His team members visits always seemed to coincide with his pill intervals and while John figured this was Beckett's ploy to make sure he was taking all his pills, the Colonel did not bother to point this out. Sheppard could easily picture each member returning to give a full report.

"Hey, Teyla." He said from his position on the bed. The volume of his voice was slightly elevated, his relief of simply having someone with him through the storm was apparent.

Grover jumped up from where he was laying next to John and ran towards the Athosian. He had learned very quickly that he loved to have his ears rubbed and he found this woman's to be his favorite, next to his friend's, of course.

"Hey, Grover!" She giggled as the once timid canine came running up to her. "Hello, John. Still feeling okay?" She asked Sheppard, while petting Grover who had sat himself on Teyla's feet to keep her in place.

"I'm doing great." John replied, only to flinch when thunder shook the room once again.

It was then that Teyla noticed the darkened windows and the man's tensed muscles.

"Would you like some music, John?" She asked, moving to Sheppard's Ipod hub and picking up the small device to begin flipping through the files.

"Sounds great." The slightly nervous smile cracked his lips while trying to ignore the harsh rain.

Within seconds the sound of Johnny Cash's 'Ring of Fire' began to mute the storm raging outside. John groaned inwardly and Teyla turned and walked up to the bed, a small sympathetic smile on her lips.

"It is perfectly understandable for you to feel uneasy during storms after what you have gone through." She said softly, as she sat down onto the mattress next to him.

Sheppard gave an uncomfortable chuckle while shaking his head slightly. "I'm not nervous, I'm just tired."

John, of course, didn't expect to truly hide this from the Athosian. The expression on her face only confirmed that she indeed did not believe him.

"Would you like me to leave you rest then?" She asked, leaving him to decide what he needed most at the moment. John wouldn't have denied that he needed sleep. He knew he looked as bad as he felt having caught a glance in the bathroom mirror earlier. So while he would have loved to have taken a fifteen minute nap, maybe for five hours, Sheppard knew he wouldn't be able to sleep with the storm outside.

"Nah, you can stay if you'd like." He replied.

Teyla smiled while shifting to make herself more comfortable with Grover firmly wedged in the middle of the them, his head laying lightly laying on John's thigh.

Any relief and comfort he found in the fact that she was staying was increased when she positioned herself between him and the window. He knew it was irrational but having someone to face the storm with was calming, after all there was not anything Teyla or anyone could do against the storm.

"Why don't you try and rest, John." Teyla said after a moments pause. "I will remain here and catch up on some reading that Torren does not seem to believe should get done."

John smiled slightly and nodded. "I'll try." He said, again not thinking he would be able to.

The Colonel inched down into the covers, burying himself as though each layer of fabric offered another shield against the world, listening as Teyla hummed along with 'Hey Jude' by the Beetles.

**Grover and him were running through the jungle, managing to keep just ahead of the people chasing him. The foliage and underbrush around them blurred as they ran only becoming more detailed when it poised to be an obstacle in their path. He knew he should be surprised due to the fact that he could keep up with the sprinting canine but he wasn't for some reason.**

**His panting rasped through the humid air but he couldn't stop. He wasn't sure why, his mind blurry with lack of oxygen, but he knew there was a good reason, it had too be. **

**Fear coursed through his body, the adrenaline giving him a much needed spur of energy, the basic instinct to survive goading him on. **

**He quickly glanced to the side to make sure Grover was still with him but he did not find the canine there and in his place was Ford. He was stumbling slightly behind him, nearly falling over with exhaustion. **

"**Do not leave me sir! Please, don't leave me with them!" **

**He stumbled to approach the Lt, hand outstretched to help him stand but he couldn't seem to reach him. With every step he took Aiden only seemed to draw farther away. **

**He yelled his name, promising the young man he would find him and never give up. Mist began to curl between them, tendrils wrapping around the soldier. He watched in horror as the tendrils transformed into hands. Ford continued to scream as they pulled him out of sight. **

**His voice grew hoarse and he fell to the ground in defeat. The damp earth beneath him was cool and quickly began to soak into his clothing, soon leaving him soaking wet. A harsh wind wiped through the thick trees and along with it came the sound of the hunting party. **

**Adrenaline burst through his veins again and he leaped to his feet, sending a spray of water in his wake. The noises were growing louder but had no defined direction which left him unsure of which way to run anymore. Spinning in a circle, trying to find the best escape route, he slowly began to make out dark figures through the mist. They were not simply in one direction though. He was surrounded with no where to run or hide. **

**The sound of a wraith stunner gave him a few seconds warning as the beam nearly grazed his ear, and he soon found himself dodging and weaving between blasts, surviving on pure chance alone. As usual, though, his luck came to a grinding halt as he was hit in rapid succession. One to the right leg another to his shoulder and he came crashing to the ground. **

**Forcing his eyes open, fighting with all his strength to last a little while longer, a face came into his field of vision. **

**"You'll never find him, Sheppard. You failed him and you failed Atlantis." **

**Koyla smirked in triumph before raising his weapon and began to laugh as he depressed the trigger.**

The cold laugh echoed in John's ears as he sat straight up in bed, startling both Grover and Teyla.

"John, is something wrong?" She asked as Grover pushed his nose into his face and whined.

"No, it was just a bad dream." He said, his heart still pounding and the adrenaline coursing through his veins, both demanding action.

Teyla's eyes softened and she laid a hand gently on his shoulder. "Would you like to talk about it?"

John shook his head. "No, maybe later." Both he and Teyla knew that his promise of later was only to avoid the conversation, which he had no intention of continuing, but they both knew this too.

"I'm starving so why don't we track down something in the mess hall?"

"That sounds like a good idea." Teyla agreed, having grown used to the Colonel's midnight hunger after sitting with him many times in the past. "But when you are finished you will go back to bed."

Sheppard gave her a lop-sided grin as she rolled his wheelchair closer to him.

**It's a little shorter but the next one will be longer, please review and let me know how I'm doing. :)**


	14. Chapter 14

Sheppard whimpered softly as he overstretched his right shoulder attempting to pull his t-shirt over his head. Frustration was near boiling as he tried again, having to sit down on the closed toilet seat to keep his balance. The Colonel nearly screamed in anger as the fabric ended up stuck, wedging his arm and face together and trapping him in darkness.

_ Loud cackling laughter echoed through John's ears, though he could see nothing through the blindfold. Calloused hands grabbed the back of his gag, as well as a fist full of hair in the process, pulling him backward. He could feel the warm trickle of blood as the skin around his mouth was torn open._

John's struggling became more desperate as the flashback began, his shoulder and back protesting greatly, before the shirt finally released him. With a sigh of relief he entered the shower, but only after stepping over Grover, who was curled up on the bathroom rug. The canine had been unwilling to let him leave his sight since their return and while Sheppard was grateful for the constant company, privacy in the restroom would have been a nice bonus.

The water was cool when first activated but Atlantis quickly adjusted it to the perfect temperature to ease John's cramping muscles.

_Thunder rumbled overhead as a torrent of luke-warm rain fell in thick sheets. Ever since his capture, John had found himself to be either soaked or damp no matter the time of day. While this may have seemed to be the least of his worries, his skin had begun to detest the conditions, breaking out into patches of an irritating rash. The rains also brought out all sorts of insects but the most worrisome was a nest just to the right of him. With each rain, what John surmised to be some sort of fire ant would swarm from the ground and attack him, as if pinning the blame on him as their home was flooded. All John could do was hope they were not poisonous and endure their assaults._

Sheppard dowsed his head under the spray, attempting to rid himself of the thousands of ants he could still feel all over his body. He quickly finished up and stopped the water, wishing to avoid any further memories. Wrapping a towel around his waist, Sheppard left the bathroom with Grover at his heels. The collie jumped into the bed, sitting erect as he watched John dress.

The Colonel had just pulled on a pair of sweat pants and was towel drying his hair when the door chime activated.

"Come on in." Sheppard called, looking around for his single clean t-shirt, grimacing slightly as the stitches still in his cheeks tugged at the skin. Carson had removed the stitches from his arm a few days before though it was still well bandaged and weak but he hadn't wanted to remove them from his cheeks yet since he had to move that skin everyday.

"Hey." Ronon said as he walked into Sheppard's living quarters.

Grover instantly perked up as he saw the Satedan entered the room, his eyes tracking every movement he made. Ronon was also was watching the dog, shifting from foot to foot, prepared for an attack. The canine still did not trust him. He was too big, too similar to his abusers for Grover to let his guard down.

"Doc..uhh, wanted me to check in, see how you were doing." Ronon spoke, finally breaking the stare.

Sheppard chuckled. "I've only been on light duty since yesterday, Ronon. How much trouble does he think I could find in my bedroom?"

The man shrugged, a smile grin on his lips. "He knows you."

"Well, I was about to grab something to eat if you wanna tag along." John grunted as he struggled to slip on a shirt, having a hard time maneuvering his shoulder.

Ronon stepped forward to help, reaching out a hand but quickly withdrawing it as a sharp bark echoed through the room.

Grover was on the floor between them.

"Grover, no!" Sheppard groaned, now trying desperately attempting to wrestle out of the confining fabric.

The canine presently sat on his haunches, teeth still bared in warning. John gave his own growl as he finally concurred his war with the garment while Ronon stood as still as possible.

"You know what, I'm sick of this." John stated as he looked at the pair of them. "Ronon, kneel down."

The Satedan gave Sheppard a disbelieving look, understandably not wanting to open himself up for an attack.

"Then you won't seem like such a threat, you know, being smaller." Sheppard explained and he slowly received a small nod from the man before he slowly sat down, being careful not to startle Grover.

"Give him some of these." Ronon was handed a pile of small biscuits. John sighed as he sat down slightly behind the mutt.

The Satedan remained quiet about his reservations, doubting this would work. In his opinion Grover was too scarred, too damaged. While Sheppard had an uncanny ability to believe in anyone's healing abilities, Ronon had a harder time. He, after all, had had his fair share of problems and while he had changed and coped, he was stretched to say he had fully healed. Healing was a process, and a very long one at that. He wasn't sure if one could overcome even their basic fear, not to mention their worst. Ronon still fought an internal battle each day. The fear of becoming a runner again was strong, a deep-seeded survival instinct, but he fought the urge to run and hide each time he faced a wraith, deciding instead to harness his need for revenge. His need to avenge his friends and family once on Sateda.

Even with his reservations, Ronon held out one of the biscuits at arms length. "Here."

The sudden movement startled Grover, who's constant low growl increased in warning.

"Gentle. Just put one in front of him, slowly." John said.

Ronon grunted and placed the treat on the floor between them much slower than his previous attempt. The three of them sat in relative silence, each waiting for the other to make a move, Grover's growls slowly tapering off.

"Now what?" Ronon grunted softly to Sheppard.

Sheppard shrugged. "Just wait, I guess."

A few more minutes passed before Grover slowly crept forward, keeping a close eye on the man in front of him before gingerly taking the biscuit by his teeth. While he would normally have gulped the food in one go if anyone else had given it to him but instead he quickly retreated further away, chewing while he still watched Ronon.

The canine finished quickly and sat down in that position, not feeling the need to return and place himself closer to the Satedan.

"Alright. Put another treat down and try to back away just a little." John said, smirking.

Shifting backwards, Ronon placed another in the same spot as before. Once again it took Grover a few moments, moving forward inch by inch. It took a few attempts until the mutt was eating each treat without retreating but he was still unwilling to take anything from Ronon's hand.

"Well, why don't we call it a day." Sheppard said after a while, stretching as he gingerly stood. "He may be full of treats but I think I need some food now that you two can be in the same room with each other."

"Sounds great." Ronon agreed, slowly rising to his feet so as not to startle Grover. "Where's your wheelchair?"

A exasperated groan broke through the Colonel's lips. Grover's ears perked up at the noise, looking from Sheppard to Ronon, unsure what this meant but having gained enough trust so as not to take it immediately as a threat to him and his friend.

"Sorry, Sheppard. I would let you but the doc gave me pretty clear orders." He said, searching through John's closet, quickly finding the collapsible wheelchair and pulling it out.

He quickly unfolded it and pushed closer to the Colonel. "Have a seat."

Grover's stubby tail began to wag in excitement, knowing he would soon be going for a walk.

"Alright, fine." John grumbled, easing himself into the seat. "What's for breakfast today anyways?"

"Not sure."

"Well as long as it's not oatmeal." Sheppard replied, as he was pushed through the door by Ronon with Grover right along side.

**Everybody please review! They are always appreciated and are almost as good as chocolate! **


	15. Chapter 15

John's room was dark, shadows creeping along the walls, seeming to lengthen as the minutes passed. Thunder clapped outside the window pane, over-powering the hard drizzle as it struck the glass. The planet's rainy season had just begun and the storms had continued to pound the city for the past few days.

A crack of lightening suddenly illuminated the entire room, revealing a small figure sitting next to the Colonel, watching as he moaned in his sleep, legs tangling in the sheets. This was the reason Teyla was there now. Days had passed since John had had a decent night's sleep. He had been plagued by nightmares; it was to be expected; but they had increased in intensity with the onset of the storms.

The bags under his eyes and his ever paling complexion did not go unnoticed by either his team or physician who gave him two choices: have a team member sit with him through the night, or have a permanent cot in the infirmary. Unsurprisingly though grudgingly he had agreed to having a guest each night once they had set up a small cot next to his bed.

Teyla smiled as she remembered how he had argued with her, insisting that she took his bed but she had eventually convinced him otherwise.

Her small smirk fell as John let out a short pained moan. Even with his occasional whimper she was reluctant to wake him, this being one of John's more peaceful moments he had had since the beginning of the week which had consisted of non-stop storms.

So here she sat, ready to wake him if his dreams grew intense.

_Sheppard screamed silently as the sharp point of a blade pressed into his sternum. He could feel the crimson droplets pooling on his chest. _

"_Not so tough now are you, Off-worlder?" The guerilla holding the silver knife sneered, twisting his wrist with delight as his prisoner hissed from behind the gag. _

_Hands tied behind his back and secured to his ankles, successfully restraining him. They had left him lying on his back, all his weight painfully crushing his arms while his shoulders blazed in agony. _

"_Tramping through the ring like you own the place. Tipping off the wraith to their next meal." The man continued to growl as John squirmed to put even a few precious centimeters between him and the cold steel. _

"_And you all expect everyone to give you a warm, friendly welcome. Well, I'm not as naive and blind as those those fools." _

_John panted, trying to pull air through the fabric while fighting through the pain as the blade carved into his flesh, the blood forming intricate designs as it flowed. _

_SGASGASGASGA_

Sheppard grimaced once again as the storm raged outside, cursing why he had managed to get captured then escape during the rainy season. It didn't allow him a moment peace. Anxiousness hung around him no matter where he was for he could either hear the patter of raindrops or he simply knew it was pouring just outside the peaceful interior of Atlantis for he could not seem to allow himself to forget.

He had been growing increasingly frustrated with himself as the days past, knowing he was never going to fully heal without facing this. As it was, he and his team were walking down the corridor toward the mess hall. Though he had been freed of his wheelchair by Carson, he held his bandaged arm close to his body and his ribs were giving him a bit of trouble, but he would be hard pressed to admit it.

Their route took them past one of Atlantis' many balconies but unlike most, this one had entirely glass doors along with a section of the wall, giving one an obstructed view of the spires of the city. Dark clouds were encompassing the entire sky while sheets of rain drenched everything. Lightening exploded in the sky to occasionally strike one of the grounding stations. The power produced by the water and wind formed an intricate dance for the world to admire.

Grover, who was of course at John's side, was not perturbed by the intense display in the least. Many people would not believed the dog capable of separating experience from environment but he seemed to have easily distinguished between the storms and his past traumatic experiences. He was even learning to over come his fear of Ronon day by day and even now was peacefully walking in the pack with him, while keeping a safe distance away.

John's hands began to shake slightly at a particularly harsh rumble of thunder. His feet felt like lead and he found himself unable to move, staring out into the storm. Memories lashed at his mind like the wind was currently striking Atlantis.

His team stood around him, having stopped when he stopped. Confusion and worry on each of their faces. Sheppard had yet to share with them anything but one would have to be blind to have not noticed the Colonel's unease during storms.

"Colonel?" Teyla said softly, placing a hand on his shoulder.

The soft touch seemed to break something and John found an anger begin to pulse through him. He was tired of the pain and his inability to do his job. Tired of the pills and the bandages. Tired of the fear. It was irrational and he wanted to be done with it.

Adrenaline surging, John bolted towards the door, running out into the pounding gale. Icy droplets assaulted his face, feeling like small daggers piercing every exposed bit of flesh. The force of such a torrent seemed to be trying to chase him back inside, attempting to beat him once again. Fighting the urge to turn tail and run from the gale, from the memories, John planted his feet. He had a firm grasp on the railing, his knuckles white. The fear that had held him for so long was still present, the memories washing over him like the raging waves below, but for the first time his anger was stronger, coming to a boiling point.

"You don't have me beat!" He screamed, leaning over the rail. "I'm not broken! You haven't won!"

Sheppard continued his rant, releasing the frustrations he had tried to stifle for so long while straining to be heard over the roar of the storm.

He fell silent after a few minutes, simply staring out into the raging sea. A shutter ran through him as his skin registered the freezing rain and sharp wind.

A sigh broke from his lips when, for the first time since returning to Atlantis the fear was not overwhelming. It was still present, a small nagging feeling in the back of his mind. He finally felt as if he was no longer broken and was instead beginning to heal.

With a small smile, Sheppard turned around to head back inside when he noticed his team standing there, simply watching him. They were soaked to the bone but none of them said anything, Rodney did however have a pinched expression as though he wanted desperately to say something but knew it was not the best time. Even Grover had remained sitting next to Teyla throughout the torrent watching John with an expression he could only assume to be confusion.

"Um, hey guys." Sheppard mumbled, embarrassed his team had witnessed his loss of control.

"Hey." Ronon replied while the rest simply nodded.

A nervous grin broke his lips as he shifted from foot to foot. "Suppose you want to talk about all that, huh?"

Teyla nodded but it was Rodney who broke his silence. "Well, I'm not sure about the rest of them but I'd like to know why I'm standing out in the ice cold rain when there's a nice hot meal waiting for me."

"Perhaps we should find a quiet place to talk, out of the rain." Teyla suggested, walking forward to take hold of his arm.

John nodded, shivering in the unending onslaught of water. "But, first we'll get you dried off." Teyla continued as she led him towards the doorway.

**Hey everyone! Sorry this is a really short chapter but I wanted to cut it here and have all the emotion talk stuff all in one chapter. I'm putting final touches on the next chapter (which usually means rewriting the whole thing) and hope to have it up by the end of the week. Please review and let me know if there is anything you would like to see in particular and I'll try and write it into the story. :)**


	16. Chapter 16

"I couldn't move." Sheppard mumbled. He had a thick blanket wrapped tightly around his shoulders, warding off the cold which seemed to have seeped into his bones.

The entire team was dry, having changed from their soaked clothing. They sat in Teyla's quarters, surrounded by the homely Athosian décor and flickering candles. Kanaan had taken Torren to New Athos to visit their people so her chambers offered a perfect sanctuary for the them to talk.

A flickering fire crackled joyfully away in the corner. It was not real but instead a very realistic hologram created by the Ancients. They had programmed it to appear as like-like as possible, producing heat (though never enough to burn) and even the light smell of burning wood permeated the room.

"They tied me, gagged me." John said in a low voice, staring into the orange flames, lost in the blaze as it lapped at the air.

_John struggled as he fought against his bonds. Thick leather dug into his flesh, blood seeping out from under each strap. The gag tearing into his cheeks had rubbed his skin raw, making the strip of fabric feel more like a strand of barbed wire. _

"I didn't have any control. Normally, they stick me in a cell or hut, so I can move around, at least some, but they kept me tied."

_A groan broke through the Colonel's lips, his shoulders aching with a smoldering pain. They were pulled tight behind him, putting continual stress on the twin joints. His hips were gripped with the same pain, bound ankles restricting their movement. John would normally have considered being locked in the a small room a bad thing, immediately trying to find a way to escape, but he would have given anything for that tiny ounce of freedom, to have had those few extra feet to move. _

"They never released me. I was tied the whole time, gagged most of it, couldn't move a muscle."

_Sheppard yelped as the sturdy boot dug into his ribs once again. His high-pitched exclamation could only be titled as that, a yelp. The Colonel had never thought himself capable of making such a sound before he had arrived in the Pegasus galaxy. Of course, he always would not have guessed he would be flying high-tech space ships and fighting terrifying space vampires either. _

_Another kick came, this one landing in his gut. He could not move, thus giving him no way to defend himself. Sheppard's captors had 'hog-tied' him that morning, securing his legs and arms behind him instead of in front. _

_Knees bent and shoulders pulled taunt leaving John's stomach and chest open for attack. _

"They killed Clarke the third day I was there." The Colonel continued to stare into the flames, not wanting to meet any of his team members in the eye. Grover was sitting on the floor, directly in front of him. Sheppard's fingers were slowly threading through the soft fur, using the feeling of each strand to help keep him grounded in reality.

_Clarke hadn't made a sound, lying silent in front of him. John swallowed, a useless attempt to bring moisture back to his mouth. He hadn't been able to tear his eyes away from the lieutenant, watching, waiting in false hope that the man would begin breathing again. He knew it was hopeless but still he could not remove his gaze, the rain gently pattering around him, creating a musical tone as it hit the leaves over head. _

_Their captors had attacked the soldier without warning, never speaking a word. They simply had untied him, threw him to the ground and begun swinging everything they had. Feet, clubs, weapons. Nothing was held back as John screamed behind his gag, trying to make the stop, begging them to stop. _

_The lieutenant had not made a noise, never screamed, never begged as he was beaten. He had simply stared at the Colonel, wanting his last sight to be of a friendly face and not one from a nightmare. _

_Deep brown eyes staring into green. That was until they closed, the strain of holding them open any longer grew to much. It had only taken another twenty minutes for Clarke to breathe his last breath, a soft, peaceful sigh and then, he was gone._

"He just stared at me, as they killed him." John mumbled, tears brimming in his eyes, but he would not let them fall. Each of his team members sat around him, each with a slightly different reaction.

Teyla was in her 'mother-mode', ready to offer comfort and healing to any who needed it. Her hand was lightly resting on John's shoulder, rubbing slow, reassuring circles.

McKay was horrified, his face pale. While many would consider the scientist to lack in imagination, instead expecting a calculating and strict mind, Rodney currently could not stop the imagines of the lieutenant bruised and bleeding, and dead in front of him. He had seen the man's body, seen the wounds, the idea of having to sit, helpless to do anything as it happened sickened him. It was something that had not occurred to him until then.

Ronon's reaction was, of course, very predictable. His anger very clear for all to see. He was mentally calculating how many rounds of C4 it would take to blow the men responsible for this to atoms when Sheppard shivered despite the blanket around him and the roaring fire.

"Perhaps you should go to bed, Colonel." Teyla said, leading him over to her and Kanaan's bed without removing her steadying hand, which had slipped down to his elbow. John more or less collapsed onto the mattress, burying deep into the thick layers of Athosian furs.

"Sleep well, Colonel." Teyla said softly, before turning to the rest of the team. Without a word, they all walked quietly towards the door.

SGASGASGASGA

Grover allowed his muscles to relax as the rest of the pack left the room. He had uneasy for hours now. His friend had confused him, first, running out into the storm then showing weakness in front of the pack. He didn't understand it. This pack was less aggressive, sure, but there was always a chance they would turn on you, trying to climb the social ladder. He had turned his back to everyone, so Grover had made sure to place himself between his friend and the pack, ready to protect him in his weakened state if need be.

Now that the pack had left however, Grover felt free to let his guard down. He jumped up onto the bed, curling up next to his friend and tucking his nose underneath his tail. He kept his ears perked, alert to any possible threat, still not entirely comfortable with the strange pack.

**You guys are slacking. 3 reviews? Three? really, guys, you can do better than that. Just let me know if you like it or not, cause I know more people are reading than three. **

**Anyways thank you JoaniexJony, Shepfan, and my ever perky, Penelope the Perky Penguin. (love your name!) My three loyal reviewers. :D  
**


	17. Chapter 17

**Sorry, this chapter may be short but I could barely find any time to finish writing it, I kinda double booked myself all week and had to run around like a chicken with my head cut off to catch up. **

**Anyways I hope you enjoy. **

John gasped as he awoke with a start, his uninjured hand raising to his chest to lay lightly over his heart. His exclamation had woken Grover, who had been pressed up against his side. The mutt whimpered, reaching up to lick the tip of Sheppard's nose in comfort, but John did not seem to notice. His face was scrunched up in a pained grimace.

His lungs were burning. Each breath he took caused a sharp stinging pain to erupt in his chest. It was different than broken or cracked ribs. A person grew very familiar with that feeling when in his career. This was something new and he would confess, terrifying. John quickly found himself struggling to draw in breath and when he did manage to: the battle began again to simply exhale.

Sheppard fumbled to grab hold of his radio on his side table, knocking over the small pile of pills he had 'forgotten' to take and his glass of water, that shattered on impact. He had convinced Rodney to leave him for the evening, feeling embarrassed by the 'baby-sitting' every night, but now he found himself wishing he hadn't.

"Inf'm'ry..help, Sh'ppa'd's qu'rt'rs." John managed to rasp into the speaker, flopping down on the mattress face first, only holding his neck up slightly so as to speak.

"Colonel Sheppard, are you all right?" The night nurse answered immediately.

Even if John had had the oxygen to reply the pain would have prevented it, leaving him to only gasp into the intercom.

"A team is on their way, Colonel." She informed him in a calm voice.

A mere few minutes passed before the infirmary staff arrived but it felt like hours to John.

"John, lad." Carson was the first to reach him, taking a quick second to check his pulse. The Scot had clearly been awoken from a deep sleep. His hair was askew and he was dressed only in red sweat pants and a loose fitting t-shirt. "What seems to be the problem, Colonel?" He asked in a calm voice, while scanning his patient head-to-toe for any obvious concerns.

"Can't-br'eth...hurts."

"All right, lad. Let's get you on the trolley." He answered hastily fitting a oxygen mask over Sheppard's nose and mouth.

If John had had the oxygen to scream he would have as his body was shifted onto the cart.

SGASGASGASGA

"What has happened to Colonel Sheppard?" Teyla asked as she and her two team mates entered the infirmary.

"He's caught quite the nasty bugger." Carson replied, running a hand through his hair.

"But you can treat him, right?" McKay said, nervously twisting his fingers together in front of him. "Should you give us medication or injections? Like antibiotics or something? I've been feeling a little feverish and-"

"I'm sure you have not contracted any sickness from the Colonel, Rodney." Teyla interrupted what was sure to be a long and drawn out list of the hypochondriac's symptoms. Colonel Sheppard must have been more susceptible due to his injuries."

"Aye, lass. We've run into a wee problem fighting the bacteria that he's contracted and with the vast number of unidentified sickness' in the database we have little hope of finding it anytime soon." Carson said, sighing.

"What are his symptoms? Perhaps Ronon or I have come in contact with such a disease."

"Nausea, tremors and pluraitis, which means that the lining of his lungs has inflamed and is causing him a great deal of discomfort with each breath. His white blood cell counts are unusually low, which tells me that his body is not recognizing the bacteria and is not taking any measures to combat it. Platelet counts are low as well, but I have no idea why yet. The whole thing is quite a puzzle."

Ronon gave a half-hearted chuckle. "Leave it to Sheppard to give you a challenge."

"Serves him right, running into the pouring rain without a coat-" McKay mumbled.

"Rodney-" Teyla scolded.

"He what?" The normally level headed doctor hissed. "Why was he out in these storms? I thought you all were caring for him?"

"He ran out onto a balcony. I wasn't about to tackle him." McKay countered.

"The Colonel was frustrated, Dr. Beckett. He simply was trying to find a release, and while it may not have been the healthiest choice, it did seem to help him in many ways."

Carson grumbled under his breath, turning away to place the computer tablet he had been carrying on the desk next to him.

"May we sit with him?" Teyla asked, attempting to break the tension.

"Not tonight, lass. I'm going to sit with him. He is in need of constant monitoring until I can guarantee his breath is not compromised." The doctor answered, the concern for his patient shining clearly in his expression.

"Can we see him now, then?" Rodney spoke up, wanting to see his friend to at least put his mind to ease for the night. A night that he would spend searching the expansive data base for such a disease that caused the Colonel's illness.

"Sure, but he is not in a very talkative mood so only for a few minutes." Carson complied, knowing it to be futile to try and keep this tight-nit team apart for long.

The group quietly made their way back to John's corner of the infirmary which was blocked by privacy curtains.

"Hey-g'ys." John managed to rasp as they entered, immediately beginning to gasp in pain due to the effort even those two words took. He frowned as the nurse who was sitting beside him adjusted the oxygen mask over his face once again.

"Shut up Sheppard, we know it hurts." Ronon grunted.

"We just wanted to check in on you and make sure you did not need anything before we return to bed." Teyla said, reaching out to grasp John's hand.

John shook his head weakly and gave her a thumbs-up without lifting his arm, not wanting to talk

"Get a good nights sleep, John. We'll be back to see you in the morning."

They were answered with a nod this time before his eyelids slipped closed.

It wasn't that he could fall asleep with the pain he was in and the conscious struggle to breath but the lighting had seemed to grow brighter by the minute, giving him a pounding migraine.

SGASGASGASGA

"Are you not going to bed, Rodney?" Teyla asked as the scientist turned down the corridor leading to his lab instead of to his quarters.

"Nah, I'm gonna search for whatever's hurting Sheppard." Rodney answered, turning to his other team mates. "Beckett said he couldn't find it so I figured I'd give it a try."

A small smirk crossed Ronon's lips while a full smile broke Teyla's expression. "That is a wonderful idea. I'll will help as well."

Ronon shrugged, before following them down the hall to McKay's lab, taking a slight detour to the mess hall to grab a pot of coffee first.

**There it is. Poor John just doesn't seem to have much luck at the moment. Please let me know what you think, you all did much better with the reviews last time. Thank you all so much!**


	18. Chapter 18

**Hey! So, this week was a little insane. The whole family has been sick (fevers of 102-103 mostly) and my sister had a wonderful ER visit from a skiing accident, no broken bones just a torn hamstring. The point is, I had very little time to type. Sorry!**

**Thanks for sticking with me for soo long! and for all the reviews!**

Teyla took a moment to rub the sleep from her eyes, removing her gaze from the glazing screen in front of her. The Athosian stood, walking over to the nearly empty coffee pot. She found the Earth beverage slightly too bitter for her to even with cream and sugar but it did make it easier to stay awake.

She and Ronon both looked up when Rodney gave a frustrated growl which turned into a yawn.

"We're not going to find anything!" McKay grumbled. "My program is sorting through all the diseases on file by symptoms but nothing is matching."

"We'll find something. Just keep looking." Ronon replied, turning back to his own monitor.

A few minutes passed without any words spoken, each person silently hoping and praying they indeed would find the solution they needed so desperately. Each felt they had faced this situation a few times too many. The Colonel seemed to always fall into trouble, no matter how hard he tried to avoid it. McKay was almost seriously considering building the man a padded room for his own protection.

"What if we don't find anything?" Teyla moaned as his manual search came up a bust once again.

"We'll find it." Ronon replied.

"But what if we don't?"

"We will, Rodney. You must not give up hope." Teyla encouraged him, walking over to place a hand on his shoulder.

"What would you do if he died?" Rodney asked in a quiet voice, his question not aimed at either of them individually but directed to both. "I mean, I think I'd stay here but I wouldn't go off-world anymore. I don't trust any of those grunts to watch my back."

Teyla smirked at his remark. "I believe I would return to my people. Raise Torren among his own tribe.

Atlantis would simply not be the same without John." She said, wiping away a single tear from her eye. "I can not imagine-"

"He'll be fine. He's stubborn." Ronon spoke again, his gruff voice surprisingly gentle and comforting.

"Yeah...yeah, he is." McKay whispered more to himself than to them.

They each lost themselves within their work once again, praying as they scanned through each disease that it would be the one they were so desperately looking for.

"Torren has been grumpy. He has not been able to see John for a while and has grown disagreeable." Teyla said, quietly.

Both Ronon and Rodney looked up at her in interest and unsurprisingly Rodney who spoke. "He's always been the favorite of all the kids." McKay huffed. "I'm the smart one after all, but do they admire brains, nope they have to like the brawn...Maybe it's the hair." The scientist mumbled to himself but loud enough for everyone to hear.

"Sheppard's nice to 'em." Ronon grunted.

"I am too!"

"John knows how to interact with him." Teyla said, scrolling through a particularly nasty sickness with a grimace.

"You mean he sinks to their level mentally." Rodney snarked, earning a smirk from both of his teammates.

SGASGASGASGA

Sheppard wanted to scream, to groan, to moan, anything to express the pain he was in but he couldn't. He had no breath to make any noise, only able to gasp with each painful intake. Shudders ravaged his body, his muscles racked with spasms, making the difficult task of breathing nearly impossible. An oxygen mask sat over his nose and mouth. They had tried a nasal cannula but he was unable to breathe through his nose, unable to draw in enough oxygen.

He felt weak, too weak to move and he could tell by the deathly pale complexion on the skin on his hand that he was anemic, a very familiar feeling for him. Despite his sorry-state, the Colonel found his left hand inching over the bed covers, searching for the comforting feel of fur at his fingertips.

Fear gripped his heart when he did not find the subject of his search. He knew his friends would not have done anything to harm Grover but he always felt safer with the mutt around, feeling that he could live through on more beating, that the unless rain was simply a drizzle, or that this sickness could easily be healed. His heart beat slowed when his fingers entangled with the soft hair of his new found friend, who's loyalty to the Colonel rivaled that of Ronon's. John smirked and he rubbed Grover's velvet ears, a cool tongue meeting his skin in greeting before the mutt settled to drift off to sleep once again.

It was only then, with the knowledge of Grover close by his side, that he realized that his mouth was dry, nearly painful from the lack of moisture gasping caused. The glint of a glass cup sitting on the table beside him caught his eye, the small ice cubes it contained glistening enticingly.

John slowly raised his arm to grab the cup but found his reach lacking. After a few more attempts, Sheppard flopped back down onto his back, concentrating solely on each breath.

"Sheppard, lad. How are you feeling? Can I get you anything?" Carson asked, his expression worried. He had thought the Colonel to be asleep, the man's breathing to have settled slightly and his tensed body falling limp.

In truth, John had not fallen into sleep. He had seen the heavy bags under Carson's eyes and the thick worry lines that creased his face so the Colonel had faked sleep to give the doctor a small respite. Keeping his breathing even slightly peaceful had almost killed him.

Instead of responding audibly, John motioned towards the glass, making a silent request.

"Oh, of course, lad." Carson said, smiling as he slipped a small ice chip into his patient's mouth.

"Now," The doctor sat down next to the Colonel's bed, taking a moment to check the various machines around John before turning to face him. "I supposed you'll want an update. Your team was up all night trying to identify whatever nasty bugger you caught doesn't seem to be in the database. They are asleep now. That took a lot of convincing, I can assure you."

John smiled at that, not doubting that at all. He knew the stubbornness of his team very well, he, after all had taught them.

"Everyone in the lab is working on finding a clue but they have yet to have any luck."

Sheppard nodded slightly, his fingers absentmindedly combing through Grover's black and white fur.

Sleep was dragging John's eyelids closed, urging his body to a much needed rest but his breathing would never give him a moments peace. Agony seared through Sheppard's chest as he failed to suppress a yawn. Carson immediately jumped to his feet with the sound of the Colonel's painful and panicking gasps.

"Calm down, lad. Just breath. Let's get you upright." The good doctor said softly, lifting his heaving patient to an upright position. "There we are.'

"Don't worry, lad. We will make you better." Carson promised, John's head resting on the doctor's shoulder in sheer exhaustion.

SGASGASGASGA

"What are we going to do?" Rodney asked as he and his team entered the conference room.

Elizabeth and Carson were already seated, though the good doctor could not seem to stay still in his chair, not pleased to be separated from his patient for even a short period.

"There was nothing in the database? Did any of the diseases even have the remotest possibility of being the one we need?" Weir asked as the team took their seat. John's chair stood empty beside her. There had been far too many times like this, as they all sat around the table, trying desperately to cure or rescue the man from himself or others.

Her question was answered by four solemn head shakes. "We've only been able to go through abouy half of the files but we haven't found anything yet."

Elizabeth sighed, running a hand through her hair. "Has there been any change in John?"

Carson shook his head. "Unfortunately not. His breathing has stabilized slightly but the strain it's causing his body has me concerned. Sleep is impossible for the lad, leaving him exhausted. If this goes on for much longer he'll be forced to rely on a breathing tube so he can get a wee bit of rest."

"Let's hope it doesn't come to that." Teyla interrupted.

"Aye, lass but I fear it may be unavoidable. His body still is not reacting to the bacteria. If we do not find a treatment soon, well, I don't see a way around this one."

Silence fell among the group, each quiet as dark thoughts echoed through their minds.

**Please review. and let's be clear, I know it's short so don't bother mentioning it. Consider me and old dog who can't learn new tricks. :)**


	19. Chapter 19

**Hey everyone, sorry it's been a really long time but I'm not gonna bother you with all the reasons. Let's just say my sister's injury is more serious than we thought and I've found a few more obligations for a while. **

**Thanks for understanding!**

Thunder roared around the Ancient city, the dark green waves that normally supported the large craft beating at her sides with intense ferocity, seemingly intent on sinking the proud structure into their depths. Rain and wind lashed at her from all directions and lightening illuminated the tall spires with each electrical charge. A lone figure stood on a small pier located on the outskirts of the Atlantis and took shelter under a small overhang near her comforting walls. He was drenched by the salty spray but it didn't bother him, as he was accustomed to the rain. Scotland, his homeland, a place of great beauty who's lush, green landscape paid testament to months of inclement weather, and he missed it sorely, even the rain. The calendar on his wall a constant reminder of the magnificent mountains and the deep fathomless lochs he'd left behind.

Carson wasn't worried about the rain, knowing from experience that Atlantis could handle the strong gale without a problem, and in many ways the weather mirrored the turbulence within himself. He was a bit of a softie, and if pushed would reluctantly admit to enjoying a number of 'chick-flicks' provided they were tasteful. Though, only to aware if he told anyone how he felt, Rodney for one, would probably never let him forget it.

Sheppard was growing worst with each passing hour, which is why he'd sought sanctuary in the storm, only too aware it might seem a strange place to some, but to a Scot like him, it was the perfect place to clear his head. He wasn't one to buckle under pressure, and had always managed to keep cool under difficult circumstances, even some of the hellish situations the relatively unknown galaxy had wrought upon the expedition. Carson aware, that even the hardiest soul could be over-whelmed by it all, though he was usually immune, until he had time to think, and that was when the worries and doubts began to creep in, like now.

Bruises had appeared on Sheppard that day, steadily getting worst with each hour. New ones that he had not acquired during his imprisonment and Carson could not find the cause of them. On top of all that his patient's organs were slowly shutting down, his body unable to hold up under the strain though it was still not recognizing the virus as something to be fought. Carson had explained it to Ronon earlier that day, saying that John's body was simply surrendering to the disease and taking no actions to fight back. A smile broke the doctor's lips when he recalled the Satedan's response. No one had ever accused Ronon of being disloyal, having never had a reason too let alone the stupidity to do so. The Satedan code of honor did not allow for a warrior to 'give-up', always expecting the soldiers to fight to the death whether the enemy could be seen or not. It had taken a few minutes for Beckett to calm the man down, Ronon having taken his statement as an insult towards his friend's honor. Carson had carefully explained his poor choice of words while attempting to be understanding of the Satedan's culture.

He was sitting with Sheppard now, keeping watch over the unconscious man. As usual, the team was taking shifts, never leaving the Colonel alone no matter the hour. While the expedition knew very little of John's life before arriving in the Pegasus galaxy even now, knowing only of his now deceased father and estranged brother, there was no doubt the lad had found a family here. A family that would do anything for him.

Beckett's thoughts turned to his own mum. He could picture her so clearly, creaking back and forth in her little rocking chair on the front porch of his childhood home that was nestled between tall mountains. The doctor's straying mind was interrupted when the hiss of the balcony door cut through the electrified air of the storm.

"Carson!" McKay's voice yelled, seemingly in competition with the thunder. "Elizabeth's been trying to reach you! We're supposed to meet in the conference room!"

Fear that something had happened to John and they had not been able to contact him rose within the good doctor but as he reached down to his pocket he found his medical pager still present but his com unit that he usually had tucked behind his ear missing. That ruled out a problem involving his patient, aside from the obvious, of course. With an internal sigh, Carson walked back into the city, wishing to have had a few minutes more in the solace of the storm but knowing that he could not allow himself that luxury just yet. Perhaps when the Colonel was well on his way to recovery the Scot would visit the mainland for a little R&R, he had a few vacation days saved up.

SGASGASGASGA

"Dr. Beckett, glad you could make it." Elizabeth said in a slightly snappish tone as McKay and Beckett entered the conference room.

"I am sorry, Elizabeth. I seem to have misplaced my com unit." The Scot replied as he sat down, taken aback by the normally composed expedition leader's hostile disposition.

Said leader seemed to notice the shocked expressions of everyone in the room as well as the tense body language of the medical department head. "No, I'm sorry Carson. I've been on edge recently." She had visited Sheppard that morning, unable to keep her gaze away from the bruising, that should have healed by now, surrounding the Colonel's eyes, mouth, and chest. They had disturbed her, to say the least. The discolored flesh in sharp contrast with the man's pale, sunken skin, giving his face the appearance of a skeleton. Along with that, the IOA was insisting of sending a group of representatives to tour Atlantis within the next week. An added concern that Elizabeth was not prepared to handle at this moment. She had learned the number one rule of the Pegasus galaxy early: The greater the importance that things go according to plan and without a hitch meant that there was always going to be trouble, and she wanted her Military Head to be on his feet and in good health before they opened that can of worms.

"We all have, Dr. Weir." Teyla spoke up, her level tone having a seemingly instant calming effect on the entire room.

Grover lay at her feet, having had to be coaxed from John's side earlier that day, stopping, if even for a moment. The canine had grown very close with the Athosian, if you did not find him with the Colonel he would be with her. Teyla had found Grover to be a wonderful companion for Torren. Playing with him with a gentleness that most humans did not possess.

"Rodney, has your search for the bacteria in the data base come up with anything?" Weir asked, her voice edged with the hope she was afraid to allow herself to feel.

The scientist answered her with a solemn shake of his head, pausing only briefly to look up at her before turning back to the screen in front of him, having begun his search as soon as he had entered the room.

"Perhaps we should return to the planet." Teyla suggested. "Might this be something he contracted there and it had not been documented by the Ancients? The locals might know of a cure."

"Is that possible?" Lorne, who had been sitting silently at the table, asked Beckett.

"It may be. Tribes on earth have developed cures for nearly everything from the jungle around them when science was not able to and considering that we haven't found anything in the database, I don't see any other solution at this point."

Few people knew, but the Scot had a few of his more youthful years in the rural jungles of Paraquay interning at a small hospital. The doctor considered those years some of the most rewarding and enjoyable moments of his entire career. In place of removing bullets from muscle and stitching the lacerated flesh back together on soldiers he had treated the sick, made house calls to the elderly, and increased the over all health of the village. It wasn't just the village, the natives came from miles to be treated at the hospital, it was, after all, one of the few in this remote corner of the world.

With every patient who had walked through the doors of the hospital came a new challenge, some of which they hadn't had any clue how to treat. The clinic had quickly learned not to dismiss the treatments the tribesmen had used for hundreds of years because, while shrouded in decades of myth, the methods were nearly always effective.

Beckett had taken an interest in cataloging each treatment, what they were made from and how they were prepared. It was a passion he had taken with him into the Pegasus galaxy, using whatever down time he had between the demands of living on a base of accident prone soldiers and scientists to research the new diseases and each possible treatment.

If he was to be honest, he had a silent dream of returning home to Scotland with a cure to one of Earth's great number of health problems.

Weir shook her head slightly. "I can not allow anyone to return to that planet. The guerilla hostiles have grown bold, the planet is now at war and because of the electrical atmosphere we can't even send in a jumper to gather any intel."

Ronon, never one to back down from a challenge, was not about to give up even the slight chance to fine a cure. "I'll go-"

"No, you won't." Elizabeth stated firmly, arms crossed in front of her. She had been expecting the Satedan response, having had to talk some sense into the man a great many times before. Today, though it did not seem like she would need to. At her refusal, Ronon had leaned back on his chair, an exhausted posture taking the place of aggression. The man had insisted on taking the 'night-shift' to sit with the Colonel, arguing that Teyla should be home with her family and Rodney needed to keep looking through the database for answers, something he would be doing anyways. The expedition leader suspected that Ronon had not bothered to sleep when he was off duty, having heard the crash of the gym mats and the Satedan's grunts at all hours of the day.

Weir turned to Beckett with a sigh. "Is there anything else we can do?"

Carson shrugged. "Aye, I have the nurses running some of the tests again, to see if anything has changed but it does not look good. I'm afraid that our hands are tied, lass. All we can do is pray for-"

The good doctor was interrupted when his pager beeped urgently. The blood drained from his face as he read the short message on the screen. "Excuse me." The ever polite Scot mumbled as he stood suddenly, knocking his chair to the ground and running from the conference room, leaving everyone else to look at each other in confusion. Confusion that quickly turned into fear and, they too, ran from the table after Beckett.

**Please review :)**


	20. Chapter 20

**Hey, sorry it took so long. Here's the next chapter. Now I know this is a little AU but just to let you know this is before the episode that Rodney gets that parasite in his brain. Hope you enjoy it. **

"What's wrong?" Carson asked quickly as he skidded on the smooth infirmary floor, nearly bowling over one of the nurses.

Kayla, one of his senior nurses, answered him. She was one of the few nurses that still remained from the original expedition, helping treat and care for John during every stay in the infirmary, there having been a great many of them throughout the years.

A highly competent nurse, she had grown close to John during his many stays in her care. Like the team, Kayla had helped Sheppard through the highs and lows, forming a relationship that could be seen clearly from the grief that shone in her eyes.

"Seizure, hemorrhaging in respiratory tract." She stated, getting straight to the point, knowing that every second was precious if they were to help the Colonel.

"Alright, someone grab me-" Beckett began to say but was cut short as a syringe was pushed into his hand by Kayla.

He smirked, injecting the drug into Sheppard's IV port, trusting the nurse completely, knowing that she would have checked and rechecked her calculations even as she walked towards them.

Almost as soon as he administered the solution, John's convulsion's ceased though blood still dribbling from his mouth and nose.

"What's going on?" Rodney asked, not knowing when to keep his mouth shut. He and the group standing a small distance to the side, remaining out of the crew's way.

"I'm not sure yet, Rodney." Carson said, a bit more sharply than he had intended, before turning back to his patient.

"Fluid in his lungs, Dr. Beckett." David Harrison, one of the military doctors, spoke up, his stethoscope pressed gently to Sheppard's chest as he listened to the crackling and rasping.

"Tap the chest, but first get an x-ray. Let's try and get an idea of what we're dealing with." The Scot replied, running a hand through his hair before turning towards the others. "I should know more once we have the radio-graphs, that will hopefully give us a plan of action. In the mean time, please take Grover." Beckett said, motioning towards the mutt who was standing underneath his friend's bed, being careful not to get under-foot while he shifted from paw to paw, understanding something to be desperately wrong but not knowing what. He needed to move to allow the nurses to unlock the rolling bed and take Sheppard to radiology.

"Grover, come." Teyla called softly. The canine was hesitant, looking up at his friend before slowly stepping out from under the bed. "Come on, Grover. They will take good care if him." She encouraged him until he walked towards her before following her out.

"Inform us the minute you have anything." Elizabeth said, before leaving as well.

SGASGASGASGA

Teyla watched helplessly as Sheppard shivered on his bed, his body gasping and coughing, desperately attempting to expel the volatile fluid that was clogging his lungs. Tears painted the Athosian's cheeks, silently running down her smooth face in moist rivulets. Though the pilot was under a medical coma, the disease over-powering the drugs in fear of escalating the pain.

Grover whined quietly from underneath the Colonel's bed where he was curled up on his thick blanket. The canine was healing as well as could be expected. A nurse had removed the bandages around his tail that morning, leaving the scabs on his small stub to dry and fall off in time.

While his body had been healing without complication, Grover had not remained the happy-go-lucky mutt he had become. With John's quickly declining health, he had grown depressed. Barely eating and only leaving his friend's side when forced.

Teyla sighed as John coughed, more dark blood spilling out of his nose and mouth, around the esophageal tube, dribbling down his chin. She reached out with a small rag to mop up the liquid which was quickly stained, the red mingling with the dried brown.

She cast a glance toward the lab, where Carson sat, head in one hand while the other fiddled with a pen, waiting anxiously for John's test results. The machine in front of him continued to chatter and whirl, seemingly longer than usual to the Scot.

He had run a multitude of tests, following a hunch. A hypothesis that left the doctor torn between hoping it proved true or not. If it was true then Beckett was about to face the biggest challenge of his career, while if the results were instead negative then they were back to square one with no treatment plan.

So here Carson was, waiting for the test results to solidify his next move.

The exhausted doctor jumped as the machine let out a high-pitched beep, startling him from his thoughts. Carson snatched the small strip of paper the moment it finished printing. As archaic as it seemed, Beckett preferred having the physical sheet to hold and mark versus the technology of Earth and Atlantis.

A low groan broke from Carson's lips when he read the results, his mind instantly listing off possible treatments and complications. He took a few minutes to gather his thoughts before touching the comm behind his ear.

"Elizabeth, there has been a development. Will you please meet me here in the infirmary?"

"Of course, Carson. I'll be there in ten minutes." She replied through the always present though faint static.

Standing up from his chair, the doctor began the preparation for the battle ahead of the Colonel. "Kayla, can you please get another chest x-ray of the Colonel. Don't bother with a lateral, the ventral/dorsal should be fine and Megan, if you would prep the surgery suite. There is a small chance the lad won't need it, but let's try to be as prepared as possible."

Both nurses immediately left to do their assigned tasks just as Teyla walked up to the Scot, having noticed all the excitement. "Have you discovered something, Doctor?"

"Aye, lass." Carson answered her, placing his hand gently on her shoulder as they walked towards Sheppard's bed once again. "If you will wait just a few minutes, Elizabeth will be here and I will explain it to both of you."

It only took a few minutes for Weir to appear followed by McKay and Ronon. "I thought they would want to hear this too." She said as they walked in.

"So what's wrong with him?" Ronon asked.

"It's a parasite." Beckett stated, pausing to look at the shocked looks on each of their faces. "Some sort of worm like creature, it's burrowed into the lining of the lad's lungs and trachea. That's what's causing the blood." He walked over to a nearby computer, pulling up John's radio-graphs.

"I noticed the slight anomalies in his first x-rays." The doctor pointed to small curving lines throughout the picture with which there was only a slight shade difference. "At first, I thought it only to be a bit of bad film or and artifact caused by the fluid build-up, but it continued to nag at me. So I ran a few tests and found that, though his leukocyte counts were not above average they were made almost entirely of eosinophils, which appear during allergic reactions and parasite infestations."

"Are you saying that, worms have invaded his lungs and are eating him from the inside out?" Rodney asked, his voice mirroring the disgust he was feeling.

"So, it's almost like Heartworm in dogs?" Elizabeth asked, remembering back to her childhood dog. His name was Blackie, not a very imaginative name by any stretch but she had been four when she had got him. The black lab had been her best friend for a few years until it was cut short by such a disease, her parents not understanding the risks they were taking by not giving Blackie the small pill once a month to prevent the parasite. The poor animal had died of heart failure one day, running through the field moments before his heart gave into the strain. Needless to say, Elizabeth had been very diligent with the medication from then on with all her other dogs.

"Very much so." Carson agreed. "Once I received the new x-ray's I'll be able to tell you more. If the lad has a lot then he'll require surgery but if there is only a few of the wee buggers, I have some medications that may do the trick."

"Do what you can, doc." Ronon stated, trusting the Scot to make the right call.

"I have every intention to, lad." Beckett replied before slipping away to see how the x-rays were going.

**So, First off just a little propaganda for Heartworm. Please get your dogs on some sort of prevention. It really is a nasty disease and very hard to treat. It's one pill once a month. Not that expensive, about $7-24 a month compared to the treatment (hundreds of dollars) Ask your vet about it!**

**I didn't have time to proof read, so let me know if I missed a word or two. **

**And like always, please review! I love hearing from all of you!  
**


	21. Chapter 21

**Well, here's the next chapter. Hope you all like it and think it was worth the wait. I was very excited I got past 2,000 words but if the chapter isn't any good and high word count doesn't mean much of anything. LOL**

"Here are the x-rays you wanted, Dr. Beckett." A radiology tech stated, handing over his computer tablet to the chief of medicine, on which the images of Sheppard's chest were already pulled up and ready.

"Thank you, Kyle." Carson replied, taking the computer from him. While the varying shades of gray did not make much sense to many people but to the Scot it was perfectly clear. The neutral gray of the tissue was interrupted by white, curving lines, taking the appearance of a child's scribbling.

"Is surgery prepared?" Carson asked without looking up from the radiographs, his eyes lingering on each pale white line, tracing their path through the lining of John's lungs. They're were so many , burrowed deep into the pilot's tissue. Too many to simply destroy the parasites with medication alone. The only answer was to surgically remove as many of the 'worms' as possible then treat whatever eggs and larva were left with the drugs. That was only once they could isolate the exact medications that would destroy the creatures without Sheppard developing any adverse reactions. The poor soldier had already been on a wide range of antibiotics and other drugs before they had discovered the large load of parasites.

"Everything is ready." Kyle answered him. "Kayla's preparing the Colonel now."

Beckett nodded in satisfaction. "Alright, give Dr. Weir a call and let her know what's happening. I'm gonna go scrub up." He sighed, standing up from his seat. "Let's hope whatever stubbornness that's kept the lad alive this long keeps it up."

SGASGASGASGA

Sweat beaded across Beckett's forehead as made another incision into his patient's chest. A monitoring machine hummed beside John's head with another nearby keeping the man breathing under the intense surgery.

"Alright, we're in." Carson said, more to himself than to his team. "I've just reached the exterior of the lungs. The worms should have absorbed the anesthetic from John's blood stream, so I'm expecting the little buggers to be at least a bit lethargic. Shouldn't be too difficult to remove."

Taking a moment, Beckett quickly checked the stability of the spreader bar that were holding the Colonel's ribs apart to allow the doctor easy access to the man's lungs. The dark tissue along each side of the ribs inflated with each breath. The purplish brown flesh was riddled with grungy white lines. This was going to take a very steady and sure hand, one that the Scot prayed he would have. Taking a quick count, Carson noted only five. Once he removed the worms he could see they would need to use the ultrasound to detect any others he may have missed.

"Do you have a container, lass?" Carson asked from behind his mask, as he gently tugged on the end of one of the smaller worms with his forceps.

"It's right here, doc." The nurse answered, holding a clear plastic container filled with formaldehyde.

Beckett nodded, sighing as he looked towards his patient, praying once more for success before beginning. "Well, here goes nothing."

Very slowly, the doctor began to pull. Inch by inch the parasite was revealed, writhing slightly. A long, thin organism. The body was smooth, much to Beckett's relief. Carson had found himself imagining large grotesque snake-like creatures with large barbs. A thing of nightmares that would be nearly impossible to remove. Once clear of the tissue, he quickly put the parasite into the jar.

The doctor smirked as the nurse in front of him shivered. "Not your cup-of-tea, is it lass?" Beckett asked as he pulled another worm from his patient's lungs, this one about two inches long, much larger than the first.

Kayla nodded minutely, wincing slightly as the doctor dropped the creature into the container she was holding with a wet plop. "It all started when I was five." She stated. "I loved anything creepy crawlies. I would try and catch anything I could. My mom hated it, making me empty my pockets before I came inside because I always tried to sneak my new pets in."

She giggled slightly, remembering her many antics as a child before continuing. "There was a patch of dirt in my neighbors yard, behind the shed. It was filled with bugs and rodents of all sorts. A swarm of ground wasps had nested there too so mom had forbidden me to go near the place. She told me again and again. Needless to say, I didn't listen."

"How many times were you stung?" Carson asked without looking up.

"Only two, but that's not what got me scared of them. There is this creature, another parasite of sorts, called a cuterebra. It's basically a fly maggot. Long story short, the thing hatched on my skin and burrowed in. I was afraid to get in trouble so I didn't tell my mom that my arm hurt for a while but when I saw it poke it's head out I knew I needed help."

"And did you get in trouble?"

"Nah, mom figured I was so terrified I would never get near any bug again." The nurse laughed. "She was right, I do everything I can to stay away from them."

"I don't blame you." Carson said, understanding how childhood trauma, no matter how mild, remained with a person for a very long time. "When I was a wee lad I accidentally locked myself in my grandmum's cellar. I wasn't found for three hours. It was filled with crickets. I know, it's a strange thing to be afraid of but a few hours in a dark, dank hole the chirpy buggers start to sound a little freaky."

Kayla nodded in sympathy, knowing that she would have been curled up, shaking, in the corner after only twenty minutes or so.

Another hour past, the doctor and the nurse continuing their small talk while removing one parasite after the other. Carson could not help but groaned as he worked his forceps around, slowly urging a particularly long worm from his burrow. Kayla grimaced as Beckett dropped the creature into the jar before she screwed the lid on tightly.

"How many more do you think are in there, doctor?" She asked as she picked up another container, standing up on her toes to peer into the open body cavity, scanning the tissue for any additional worms.

"Not in this section of the lungs but I saw a few of the crafty buggers hiding out in the trachea." Carson replied, scanning the x-rays on the table beside him for any that he might have missed. "How many do we have so far?"

"21."

The Scot nodded, using his forceps to peer into the trachea. "Would you hand me the endoscope?" He quickly found said instrument in his hand. One by one he pulled out the worms, being careful so as not to damage any of the surrounding tissue in the process.

"Well, that's that section, now for the other lung." Beckett sighed as he began to stitch up the incision.

SGASGASGASGASGA

"How is the Colonel, Doctor Beckett? Elizabeth asked as Carson walked through the doorway, the doctor looking exhausted but somewhat positive.

"He doing very well, actually. Twenty-nine of those little buggers had made their homes in the lad. We removed 'em and, even with the damage done to his lungs, John's breathing has improved greatly but he will still need to be on the ventilator for a few more days at least."

"Twenty-nine?" Elizabeth asked, shivering slightly, having always been 'creeped out' by anything with more or less than two or four feet.

"Aye." Carson nodded. "Poor lad had a payload."

"But how did they get inside?" Ronon asked, who had been sitting in the corner of the waiting room for the last fifteen minutes. It had been decided that due to the expected long duration of this surgery, that the team would take shifts, much like they had during Sheppard's recovery. The Satedan had already contacted Rodney and Teyla so that they could also hear what the doctor had to say.

Beckett nodded. "Now, that's the mystery but I'll hazard a wee guess. The lad was covered with a multitude of insect bites when he returned. Many, of which, seemed to come from the same buggers. I would suspect that these insects, when they bit the Colonel, transferred the parasite."

"But that was in the skin. How did they get to the lungs?" Weir asked.

Carson grinned slightly, having loved his parasitology class in medical college. "Parasites often do not remain in the same portion of the body they entered, instead migrating to their preferred location."

The 'bug' lesson was interrupted by the entrance of Teyla and Grover, the latter of which immediately ran up to the group, focusing on Elizabeth in particular. The expedition leader had not had a lot of time to spend with the mutt these passed few days, having been too busy dealing with the up-coming financial reports and preparing for her 'small' trip back to Earth.

"Hey buddy." She said, leaning down to pet the excited border collie. She paused when she noticed a dime-sized bump underneath his eyelid. "What's under his eye?"

"I was, actually, on my way to ask you, doctor," Teyla replied, "when I received Ronon's message. I'm sorry, I did not noticed it before."

"Well, let's take a look now, shall we?" Carson said, kneeling down and motioning Grover over to him, who gladly complied.

While Grover had learned to trust most people, he still was nervous whenever they drew close to his eyes or feet, those being his more sensitive and vulnerable spots, so the doctor had to settle with looking at the strange lump from a distance. Even though he was unable to get very close while petting the canine, he had a strong hunch of what this new growth truly was.

"Bridget." Beckett called to one of the nearby nurses. "Could you prepare surgery once more for Grover here."

"Sure thing, doc." The nurse replied before walking away.

"What is it, Carson?" Teyla asked.

"Most likely the same buggers that were causing the Colonel such grief."

"But they were in his lungs." Elizabeth stated in confusion. "Why would they be in Grover's eye?"

Carson nodded, continuing to scratch the mutt's ears. "You remember when I said the parasites migrated to the lungs well, parasites do not always 'choose' the same location in different species so while they made their home in the poor lad's lungs they seemed to find Grover's eye a bit more appealing."

This time Elizabeth and Teyla, both, had to repress a shiver, the thought of small worms burrowing into an eye enough to turn anyone's stomach.

"The Colonel should be out soon. The lad will still have some problems breathing so the respiratory tube will need to stay in place for a wee while longer. We're gonna slowly wake him up to reduce the stress on his body but you can start with the schedule again. The doctor continued, as he gathered up Sheppard's x-rays as well as his small computer tablet. "Now, if you don't mine, I have another surgery to complete."

The group nodded as he walked out of the waiting room.

"I will contact Rodney and let him know." Teyla said, it being the Canadian's turn to sit with the CO.

"Let me know what?" McKay asked, quickly walking in at that moment.

"I will fill him in." The Athosian stated, turning to Ronon and Elizabeth before they headed out the door.

SGASGASGASGA

Carson sighed as he watched both his patients' chest rise and fall with each deep breath in their sleep. Sheppard had woken only a few hours before but despite the tube in his throat the pilot was too exhausted and weak to attempt speech just yet. Grover had woken much quicker than John, his surgery having been much simpler. They had pulled five smaller parasites from the canine's left eye, but no serious damage had been done so Carson expected Grover to recover completely and have no lasting sight lose.

Beckett's hand rose unconsciously to run through his hair as he stifled a yawn, wanting nothing more than to join the Colonel in his sleep. Teyla, who had been on 'sitting duty' last had tried to convince him to retire to his bed but Carson needed to sit with the Colonel until he was fully aware, if not for John's own good, for his nurses were highly capable, but for his own. Sheppard had had so many unexpected set backs in the past few years, Beckett wanted to make sure another nasty surprise didn't sneak up on them.

The fact that he was sleeping however told Carson that they were, in fact, over the worst of it. Now, the only thing in front of Sheppard was the very long and tiring road to recovery. A hard journey for the pilot but Carson and the team would be there for him every step of the way.

**Thanks for reading! The next chapter will be the last so please review but no flames. :)**


	22. Chapter 22

**Here's the last chapter/snippet/epilogue. It's not very long, so I'm sorry about that but I rewrote this a million times and this seemed to be the best way to wrap it up. **

Beckett nearly moaned as he leafed through yet another medical journal, having finished all the paperwork he could that day, and with no patients the doctor was understandably bored.

He only had three nurses on duty, with a few more on call, sat nearby tinkering and cleaning the medical equipment in order to fill their own time.

The last week had been a slow one, leaving Carson wishing for a wee bit of excitement, a problem to focus on. However, the Scot found that with each of these thoughts his mind was drawn back to his most recent patient, a one Lt. Col. John Sheppard, the bane of the good doctor's existence.

It had been almost twenty-four since the pilot had last been in the infirmary, a routine check-up this time to see how John was faring after the complicated surgery he had undergone only a week ago. His breathing had greatly improved even by day after the procedure but the holes in his lungs tissue was going to take a good deal of time to fully heal, leaving the Colonel out of breath even during the simplest of activities. Because of this, Carson, having given into Sheppard's constant moaning, released him from the ward but confined him to a wheelchair, one that he was not to vacate for any reason. With a few well stated threats given to Sheppard, Teyla had reported him to have been a very cooperative patient for once but Carson knew it had more to do with the man's depleted energy than his willingness to obey. The lad had always been a free spirit.

Beckett groaned once more as he looked at the clock. Sheppard was now almost thirty minutes late to have his stitches removed. He hadn't done it yesterday, wishing to give the skin one more day to heal, considering the trauma it alone had under gone only recently.

The doctor was just about to try and contact John through his comm link when he remembered the comms were down, Rodney saying something about rewiring something-or-other, to be honest, he hadn't really been listeing. Standing up from his seat, Carson decided to find his wayward patient, informing the nurses to page him if anything were to change.

It dd not take long for him to run into Ronon and Teyla, who was holding Torren.

"Have either of you seen the Colonel?" He asked them.

Both shook their heads but it was Teyla who spoke. "We were on our way to meet him after his appointment for lunch. Did he not show up?"

"No, lass, he didn't. I suppose I should go and find him."

Ronon was about to offer to help when Major Lorne ran up to the group.

"Doc, Colonel Sheppard needs you."

"What's wrong?" Beckett asked, a little worried as multiple situations popped into his mind.

Lorne slowly grinned. "Well, apparently, the Colonel was tired of pushing himself around so he MacGyvered a way for Grover to pull him. That mutt really likes to run. He got going too fast through the halls, crashed into the Gate Room and bowled over a few scientists." Evan shrugged before continuing. "Finally stopped when the wheelchair tipped. Sheppard claims he's fine but Elizabeth won't let him move until you check him out."

Carson gave out a good tempered groan, looking over to Teyla who was grinning and to Ronon who was trying to withhold his laughter.

"I'll go grab my kit." He stated, knowing from the Major's tone that this was nothing serious. With a small medical bag in hand, the Scot made his way to the Gate Room, wishing everyday could be like today with only minor scrapes and bruises but he knew that for as long as Lt. Col. John Sheppard was on Atlantis things would never be boring.

**Thanks again to everyone who reviewed and kept up with me! Please don't forget to review one more time! And I am sorry how long it took me to update throughout the story, I know it drives me crazy when the stories I'm reading don't update regularly and I just want to thank you for being so patient and understanding!**


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